QoS - SCCP vs. SIP

Sure.  The QoS settings apply to both the SCCP and SIP VoIP traffic.  As I said, the CME SCCP is flawless during file downloads while a simultaneous SwitchVox SIP call is severely chopped up.

The QoS portions of the config follow.  I look for any CS5 marked traffic or anything originating from the SwitchVox server (10.0.0.16) or the SIP phone (10.0.0.121) and remark it as EF as it goes out through the LAN interface.  The WAN interface policy looks for anything going out marked EF and puts it iin the priority queue.  At the same time, the WAN interface polices FTP/HTTP inbound to reserve bandwidth for voice.

class-map match-any FTP-Traffic
 match protocol ftp
 match protocol http
 match protocol secure-http
 match protocol secure-ftp
class-map match-any CS5
 match ip dscp cs5
 match access-group name switchvox-server
 match access-group name switchvox-phone
class-map match-any VOICE
 match ip dscp ef
class-map match-any Signaling
 match ip dscp cs3
 match ip dscp af31
class-map match-any INTERNETWORK-CONTROL
 match ip dscp cs6
 match access-group name IKE
class-map match-any TRANSACTIONAL-DATA
 match ip dscp af21  af22
policy-map Limit-FTP
 class FTP-Traffic
   police cir 16000000
     conform-action transmit
     exceed-action drop
policy-map MARKING
 class CS5
  set dscp ef
policy-map V3PN-EDGE
 class VOICE
    priority percent 33
 class INTERNETWORK-CONTROL
    bandwidth percent 5
 class TRANSACTIONAL-DATA
    bandwidth percent 21
    queue-limit 20 packets
 class SCAVENGER
    bandwidth percent 1
    queue-limit 1 packets
 class Signaling
    bandwidth percent 5
 class class-default
    fair-queue
     random-detect
interface FastEthernet0/0
 description connected to Private LAN
 ip address 10.0.0.1 255.255.255.0
 ip nat inside
 ip virtual-reassembly
 zone-member security ZN-Inside_LAN
 ip tcp adjust-mss 1300
 duplex auto
 speed auto
 service-policy input MARKING
interface FastEthernet0/1
 description Cable modem
 bandwidth 2200
 ip address w.x.y.z 255.255.255.240
 ip nat outside
 ip virtual-reassembly
 zone-member security ZN-Outside_T1
 duplex auto
 speed auto
 crypto map combinedmap
 service-policy input Limit-FTP
 service-policy output V3PN-EDGE
ip access-list extended switchvox-phone
 permit ip host 10.0.0.121 any
ip access-list extended switchvox-server
 permit ip host 10.0.0.16 any

The first thing I would do is make sure you are getting matches on the acls when you make a call.  Next I would get a trace and look at the packets and make sure they are being marked appropriately with dscp on the far end.  Then post the results.  

Also check out this config:
https://www.myciscocommunity.com/message/5883%3Bjsessionid=4DE16FE2C2E469E0041E4AA0CEADDF90

Here are some counters that demonstrate packets are being marked and evaluated by the routers.  

Local#sh  policy-map interface
 FastEthernet0/0

  Service-policy input: MARKING

    Class-map: CS5 (match-any)
      4345 packets, 978661 bytes
      5 minute offered rate 34000 bps, drop rate 0 bps
      Match: ip dscp cs5 (40)
        0 packets, 0 bytes
        5 minute rate 0 bps
      Match: access-group name switchvox-server
        4345 packets, 978661 bytes
        5 minute rate 34000 bps
      QoS Set
        dscp ef
          Packets marked 4345

    Class-map: class-default (match-any)
      32415 packets, 2768899 bytes
      5 minute offered rate 166000 bps, drop rate 0 bps
      Match: any
 FastEthernet0/1

  Service-policy input: Limit-FTP

    Class-map: FTP-Traffic (match-any)
      69885 packets, 90475434 bytes
      5 minute offered rate 3979000 bps, drop rate 0 bps
      Match: protocol ftp
        0 packets, 0 bytes
        5 minute rate 0 bps
      Match: protocol http
        69136 packets, 89962823 bytes
        5 minute rate 3952000 bps
      Match: protocol secure-http
        749 packets, 512611 bytes
        5 minute rate 11000 bps
      Match: protocol secure-ftp
        0 packets, 0 bytes
        5 minute rate 0 bps
      police:
          cir 16000000 bps, bc 500000 bytes
        conformed 69885 packets, 90475434 bytes; actions:
          transmit
        exceeded 0 packets, 0 bytes; actions:
          drop
        conformed 10391000 bps, exceed 0 bps

    Class-map: class-default (match-any)
      7168 packets, 1548510 bytes
      5 minute offered rate 62000 bps, drop rate 0 bps
      Match: any

  Service-policy output: V3PN-EDGE

    queue stats for all priority classes:
      Queueing
      queue limit 64 packets
      (queue depth/total drops/no-buffer drops) 0/0/0
      (pkts output/bytes output) 4628/1297104

    Class-map: VOICE (match-any)
      4628 packets, 1038927 bytes
      5 minute offered rate 38000 bps, drop rate 0 bps
      Match: ip dscp ef (46)
        4628 packets, 1038927 bytes
        5 minute rate 38000 bps
      Priority: 33% (726 kbps), burst bytes 18150, b/w exceed drops: 0


    Class-map: INTERNETWORK-CONTROL (match-any)
      23 packets, 2116 bytes
      5 minute offered rate 0 bps, drop rate 0 bps
      Match: ip dscp cs6 (48)
        23 packets, 2116 bytes
        5 minute rate 0 bps
      Match: access-group name IKE
        0 packets, 0 bytes
        5 minute rate 0 bps
      Queueing
      queue limit 64 packets
      (queue depth/total drops/no-buffer drops) 0/0/0
      (pkts output/bytes output) 23/3082
      bandwidth 5% (110 kbps)

    Class-map: TRANSACTIONAL-DATA (match-any)
      0 packets, 0 bytes
      5 minute offered rate 0 bps, drop rate 0 bps
      Match: ip dscp af21 (18) af22 (20)
        0 packets, 0 bytes
        5 minute rate 0 bps
      Queueing
      queue limit 20 packets
      (queue depth/total drops/no-buffer drops) 0/0/0
      (pkts output/bytes output) 0/0
      bandwidth 21% (462 kbps)

    Class-map: SCAVENGER (match-all)
      2 packets, 330 bytes
      5 minute offered rate 0 bps, drop rate 0 bps
      Match: ip dscp cs1 (8)
      Queueing
      queue limit 1 packets
      (queue depth/total drops/no-buffer drops) 0/0/0
      (pkts output/bytes output) 2/120
      bandwidth 1% (22 kbps)

    Class-map: Signaling (match-any)
      83 packets, 6336 bytes
      5 minute offered rate 0 bps, drop rate 0 bps
      Match: ip dscp cs3 (24)
        83 packets, 6336 bytes
        5 minute rate 0 bps
      Match: ip dscp af31 (26)
        0 packets, 0 bytes
        5 minute rate 0 bps
      Queueing
      queue limit 64 packets
      (queue depth/total drops/no-buffer drops) 0/0/0
      (pkts output/bytes output) 83/10802
      bandwidth 5% (110 kbps)

    Class-map: class-default (match-any)
      35547 packets, 2759527 bytes
      5 minute offered rate 158000 bps, drop rate 0 bps
      Match: any
      Queueing
      queue limit 64 packets
      (queue depth/total drops/no-buffer drops/flowdrops) 0/0/0/0
      (pkts output/bytes output) 35542/2955648
      Fair-queue: per-flow queue limit 16
        Exp-weight-constant: 9 (1/512)
        Mean queue depth: 0 packets
        class     Transmitted       Random drop      Tail/Flow drop Minimum Maximum Mark
                  pkts/bytes    pkts/bytes       pkts/bytes    thresh  thresh  prob

        0           43127/3989545         0/0              0/0                 20            40  1/10
        1               0/0               0/0              0/0                 22            40  1/10
        2               0/0               0/0              0/0                 24            40  1/10
        3               0/0               0/0              0/0                 26            40  1/10
        4               0/0               0/0              0/0                 28            40  1/10
        5               0/0               0/0              0/0                 30            40  1/10
        6               0/0               0/0              0/0                 32            40  1/10
        7               0/0               0/0              0/0                 34            40  1/10
 

I do not see the sip marking in the config.  I may be missing it though.
class-map match-any sip
match ip dscp cs3
match protocol sip

As part of my troubleshooting, I'm taking all IP from the server and marking it EF.  The log I posted proved to me that the voice packet were seen by the VOICE class map on both sides.

class-map match-any CS5
 match access-group name switchvox-server
policy-map MARKING
 class CS5
  set dscp ef

When troubleshooting something like this with qos be as specific as possible.  I would remove the acl and specifically mark the sip traffic.  As a note sip will use tcp or udp depending on the application.