Xen Server Storage Issue

I'm sure you tried right clicking the storage and elect "repair". What did that do?
Have you checked the log files on your upgraded host?
You'll find the important ones here:

/var/log/messages
/var/log/xensource.log

You can use a tool like WinSCP to connect to the Dom0 and look at the content.
Check for any errors, especially around boot time, and post back.

Yes, I tried repair - the error mentioned PBDs

/var/log/messages mentioned:
very big device

xensource.log extract attached, where it tries to attach the SR. PBD is mentioned in here also.

Thanks for the quick reply by the way.
xensource-extract.txt

Try to look up the messages in SMLog, right around the time the xensource log reported the error. SMlog is located in the same folder /var/log/
I forgot that storage operations are mostly logged in SMLog.

Extract below, but the full file is attached:

[14279] 2012-12-22 22:50:51.246524	SUCCESS
[14279] 2012-12-22 22:50:51.246669	Synching Metadata volume
[14279] 2012-12-22 22:50:51.246766	['/usr/sbin/lvchange', '-ay', '/dev/VG_XenStorage-25b74c46-b305-c164-1070-6bf5abb49c5b/MGT']
[14279] 2012-12-22 22:50:51.341808	SUCCESS
[14279] 2012-12-22 22:50:51.342376	lock: released /var/lock/sm/25b74c46-b305-c164-1070-6bf5abb49c5b/sr
[14279] 2012-12-22 22:50:51.351858	***** sr_attach: EXCEPTION exceptions.AssertionError, 
  File "/opt/xensource/sm/SRCommand.py", line 94, in run
    return self._run_locked(sr)
  File "/opt/xensource/sm/SRCommand.py", line 131, in _run_locked
    return self._run(sr, target)
  File "/opt/xensource/sm/SRCommand.py", line 223, in _run
    return sr.attach(self.params['sr_uuid'])
  File "/opt/xensource/sm/LVMoHBASR", line 124, in attach
    LVHDSR.LVHDSR.attach(self, sr_uuid)
  File "/opt/xensource/sm/LVHDSR.py", line 309, in attach
    self._checkMetadataVolume(self.sm_config)
  File "/opt/xensource/sm/LVHDSR.py", line 201, in _checkMetadataVolume
    self._synchMetaData(map)
  File "/opt/xensource/sm/LVHDSR.py", line 211, in _synchMetaData
    xml = metadata.retrieveXMLfromFile(self.mdpath)
  File "/opt/xensource/sm/metadata.py", line 103, in retrieveXMLfromFile
    _testHdr(hdr)
  File "/opt/xensource/sm/metadata.py", line 41, in _testHdr
    assert(hdr[2] <= MD_MAJOR)

[14279] 2012-12-22 22:50:51.357473	lock: closed /var/lock/sm/25b74c46-b305-c164-1070-6bf5abb49c5b/sr
[14451] 2012-12-22 22:50:51.373612	LVMCache created for VG_XenStorage-76c86946-ce7a-6690-ba60-2692a0b5e303
<14451> 2012-12-22 22:50:51.514441	Host f8b94db1-26eb-4bcb-96ac-293075c52204 not enabled
<14451> 2012-12-22 22:50:51.514677	Pool is not ready, exiting
<14451> 2012-12-22 22:50:51.514750	SR 76c8 ('NetApp 2.5TB 1st floor') (0 VDIs in 0 VHD trees): no changes
[14491] 2012-12-22 22:50:51.699425	LVMCache created for VG_XenStorage-c06d1738-f71a-4b4a-d7df-3685db30e2a8
[14491] 2012-12-22 22:50:51.708770	['/usr/sbin/vgs', 'VG_XenStorage-c06d1738-f71a-4b4a-d7df-3685db30e2a8']
[14491] 2012-12-22 22:50:51.841909	SUCCESS
[14491] 2012-12-22 22:50:51.842105	lock: acquired /var/lock/sm/c06d1738-f71a-4b4a-d7df-3685db30e2a8/sr
[14491] 2012-12-22 22:50:51.842172	LVMCache: will initialize now
[14491] 2012-12-22 22:50:51.842218	LVMCache: refreshing
[14491] 2012-12-22 22:50:51.842288	['/usr/sbin/lvs', '--noheadings', '--units', 'b', '-o', '+lv_tags', '/dev/VG_XenStorage-c06d1738-f71a-4b4a-d7df-3685db30e2a8']
[14491] 2012-12-22 22:50:51.921928	SUCCESS
[14491] 2012-12-22 22:50:51.922361	lock: released /var/lock/sm/c06d1738-f71a-4b4a-d7df-3685db30e2a8/sr
[14491] 2012-12-22 22:50:51.922611	lock: closed /var/lock/sm/c06d1738-f71a-4b4a-d7df-3685db30e2a8/sr
[14491] 2012-12-22 22:50:51.922684	LVMCache created for VG_XenStorage-c06d1738-f71a-4b4a-d7df-3685db30e2a8
[14491] 2012-12-22 22:50:51.932351	['/usr/sbin/vgs', 'VG_XenStorage-c06d1738-f71a-4b4a-d7df-3685db30e2a8']
[14491] 2012-12-22 22:50:52.008071	SUCCESS
[14491] 2012-12-22 22:50:52.008258	lock: acquired /var/lock/sm/c06d1738-f71a-4b4a-d7df-3685db30e2a8/sr
[14491] 2012-12-22 22:50:52.008326	LVMCache: will initialize now
[14491] 2012-12-22 22:50:52.008371	LVMCache: refreshing
[14491] 2012-12-22 22:50:52.008442	['/usr/sbin/lvs', '--noheadings', '--units', 'b', '-o', '+lv_tags', '/dev/VG_XenStorage-c06d1738-f71a-4b4a-d7df-3685db30e2a8']
[14491] 2012-12-22 22:50:52.147745	SUCCESS
[14491] 2012-12-22 22:50:52.148196	lock: released /var/lock/sm/c06d1738-f71a-4b4a-d7df-3685db30e2a8/sr
[14491] 2012-12-22 22:50:52.148327	lock: acquired /var/lock/sm/c06d1738-f71a-4b4a-d7df-3685db30e2a8/sr
[14491] 2012-12-22 22:50:52.148461	sr_attach {'sr_uuid': 'c06d1738-f71a-4b4a-d7df-3685db30e2a8', 'subtask_of': 'OpaqueRef:94fadc0d-5104-cea7-8f83-46c3f9ab1b5c', 'args': [], 'host_ref': 'OpaqueRef:a69330e3-757f-8ff5-6099-d397d54caf85', 'session_ref': 'OpaqueRef:e1791520-24a6-f91e-3670-373e4153111f', 'device_config': {'device': '/dev/disk/mpInuse/360a98000572d5038636f58795a6c3753', 'SCSIid': '360a98000572d5038636f58795a6c3753', 'SRmaster': 'true'}, 'command': 'sr_attach', 'sr_ref': 'OpaqueRef:ac0b5d46-1ac7-7051-83c0-d1e720b5779f'}
[14491] 2012-12-22 22:50:52.148766	lock: acquired /var/lock/sm/c06d1738-f71a-4b4a-d7df-3685db30e2a8/running
[14491] 2012-12-22 22:50:52.148830	lock: acquired /var/lock/sm/c06d1738-f71a-4b4a-d7df-3685db30e2a8/sr
[14491] 2012-12-22 22:50:52.158463	RESET for SR c06d1738-f71a-4b4a-d7df-3685db30e2a8 (master: True)
[14491] 2012-12-22 22:50:52.195078	lock: released /var/lock/sm/c06d1738-f71a-4b4a-d7df-3685db30e2a8/sr
[14491] 2012-12-22 22:50:52.195159	lock: released /var/lock/sm/c06d1738-f71a-4b4a-d7df-3685db30e2a8/running
[14491] 2012-12-22 22:50:52.195211	lock: closed /var/lock/sm/c06d1738-f71a-4b4a-d7df-3685db30e2a8/sr
[14491] 2012-12-22 22:50:52.195261	lock: closed /var/lock/sm/c06d1738-f71a-4b4a-d7df-3685db30e2a8/running
[14491] 2012-12-22 22:50:52.202113	set_dirty 'OpaqueRef:ac0b5d46-1ac7-7051-83c0-d1e720b5779f' succeeded
[14491] 2012-12-22 22:50:52.202177	MPATH: multipath activate called
[14491] 2012-12-22 22:50:52.202227	['/opt/xensource/sm/mpathHBA', 'enable']
[14491] 2012-12-22 22:50:52.221720	SUCCESS

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SMlog.txt

From /var/log/messages

Dec 22 22:50:51 bcxenhostb3 fe: 14283 (/opt/xensource/sm/LVMoHBASR <methodCall><methodName>sr_scan</methodName><para...) exitted with code 0
Dec 22 22:50:51 bcxenhostb3 fe: 14279 (/opt/xensource/sm/LVMoHBASR <methodCall><methodName>sr_attach</methodName><pa...) exitted with code 1
Dec 22 22:50:51 bcxenhostb3 xapi: [error|bcxenhostb3|0 thread_zero|creating storage D:aeefcbfe0dce|xapi] Could not plug in pbd '8f3869e9-38c6-e041-da4e-5a21ae84dc61': Api_errors.Server_error("SR_BACKEND_FAILURE", _)
Dec 22 22:50:52 bcxenhostb3 multipathd: sdam: add path (operator)
Dec 22 22:50:52 bcxenhostb3 multipathd: sdam: spurious uevent, path already in pathvec

Unfortunately, there is not much info in the file that I could help you with. I would highly suggest you open an account with the official citrix forum and post your file outputs there if not already done so.
There are Citrix employees on these forums that might be able to help you further.

Also, I assume you disabled HA on your Server before doing the upgrade? How about Multipathing? If Multipathing is still active on your xenservers, try disabling that on all of them and then try to attach the storage again.

Thanks, I have posted all of this information over there to see if anything comes out of it,

HA isn't licensed as it is the free version of xenserver, unsure on multipathing? This only affects the one I upgraded to 5.6 from 5.5, so I still have the option to rollback, and try again I suppose.

Yes, you can start over, especially if you have run a "Xe pool-dump-database" and saved the resulting file somewhere offsite.
Then you can simply reinstall the old version and run the restore of the PoolDB on that host.

Do i have to restore the DB? I have reverted the pool master back to 5.5 but still have the SR issue

check if the Ip address of the storage or the account used is changed.

Its FC storage

Correct steps to resolve the sr not appearing.