Exchange 2003 and IMF Delayed Emails

I been having problems recently receiving emails in a timely manner from a particular sender.  Sometimes they will come straight through and sometimes they may be delayed 4 - 45 minutes. There were a rare couple delayed for 4 days.   Through some tracing I notice the delays are happening through my Exchange 2003 Server.

Please also note I am also running IMFCompanion.  I have also added this senders email address to the IMFCompanion "Whitelist" as their emails were sometimes getting trapped.  

I looked through the Exchange 2003 Message Tracking Center to verify the times.
One example email that is delayed shows in Message Tracking Center:
3:01PM SMTP:Message Archived By Intelligent Message Filtering
3:01PM SMTP:Messege deleted by Intelligent Message Filtering
3:41PM SMTPMessage Submitted to Advanced Queuing
...  
3:41PM SMTP Store Driver: Message Delivered Locally to Store to (address)

Between the message being deleted from Intelligent Message Filtering to being Submitted to Advanced Queuing, there is the delay.   By my understanding the email is sent by IMFCompanion to its "pickup" folder located at exchsrvr\mailroot\vsi 1\pickup.  I am assuming that since the senders address is on the "whitelist", that the email gets moved to that "pickup" folder and then Exchange comes in and picks up that emails and delivers.   As I mentioned also, there is a variation of time delivery.  If that "pickup" folder were to populate with a lot of emails or some other Exchange functions are going on, then that could create the delays in sending out those emails also, correct?
I COULD BE WRONG ON THE ABOVE.   Anyone with knowledge on how this works please let me know.
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I took the headers from different emails sent in.  Some have SCL ratings and the received portion being received by MAIL PICKUP SERVICE.   I notice those ones have delays.

Microsoft Mail Internet Headers Version 2.0
Received: from mail pickup service by mail.barcouniforms.com with Microsoft SMTPSVC;
             Tue, 27 Oct 2009 13:56:22 -0700
X-SCL: 7 90.95%
Received: from mail.all-travel.com ([207.93.71.5]) by mail.barcouniforms.com with Microsoft SMTPSVC(6.0.3790.1830);
             Tue, 27 Oct 2009 13:52:11 -0700

Other emails from the same sender are not delayed and not picked up as being Spam:

Microsoft Mail Internet Headers Version 2.0
Received: from mail.all-travel.com ([207.93.71.5]) by mail.barcouniforms.com with Microsoft SMTPSVC(6.0.3790.1830);
             Tue, 20 Oct 2009 15:36:49 -0700
X-WatchGuard-Mail-Exception: Allow
MIME-Version: 1.0
Content-Type: multipart/mixed;
            boundary="----_=_NextPart_001_01CA51D5.F5E92864"
Subject: FW: barco ~ Blackburn
Date: Tue, 20 Oct 2009 15:37:52 -0700
Message-ID: <95F23475EB426245A83596A6BE6678550237B686@AT4.alltravel.local>
X-MS-TNEF-Correlator:
From: <address>
To: <address>
Return-Path: vickidr@All-Travel.com
X-OriginalArrivalTime: 20 Oct 2009 22:36:50.0038 (UTC) FILETIME=[D0703960:01CA51D5]

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My questions are:

1.  Am I correct in saying that the delays are happening at the PICKUP folder ... or am I off?

2.  Why are some emails being seen as spam and some are not when they are coming from the same sender address and IP address?

Thanks for any help or advice you can throw my way.

Greg Ho