Adobe Media Encoder CS5 hangs when adding files of varying HD resolutions.

I've seen questions similar to this related to CS4 but never explained very well, and my CS4 for mac worked fine.  I am unsure if this is a new problem or a windows specific problem but here is the situation, if you need more information I will gladly provide it.
For the past week or so I have been encoding 1920x1080i mov files (h.264/aac) to 1280x720p (vp6/mp3) flvs.  When I stick to that single HD format in the AMC processing que everything works great. However, when I add older HD content into the AMC que, content with non-standard presets, the program hangs.  I tried to import about 15 files last night and the program just sat there all night in a '...NOT RESPONDING' state.  The video's have different audio and video settings and it's little difficult to pinpoint exactly what they were.  Some are 1440x1080, some are 1280x900, some have PCM audio some of mp3. 
Now I temporarily resolved this issue by simply using cs4 master on my mac pro which worked great.  However I have noticed a huge speed increase in CS5 64bit AMC.  It takes 2-3 hours to encode 1 flash video on my mac pro (dual quad core xeon 2.9Ghz/32GB ram) with CS4.  It takes ~20 minutes on my windows 7 station (single core 2 quad 3Ghz/8GB ram) with CS5.
How to replicate:
If I drop a single file into the AMC CS5 que, regardless of the resolution, frame rate, or sound codec; it will import.  If I then add another file with a different resolution AMC will hang and become non-responsive.  It never crashed but I can't wait 12+ hours to see if it accepted a job or not.  As I said before this problem was not observed on CS4 for mac - it worked flawlessly, albeit a little slow. 
Software used:
Adobe Media Encoder CS5 windows 64bit
Adobe Media Encoder CS4 mac 32bit
System specs:
Windows 7 home:
Core 2 quad 3Ghz
8GB ram
80GB SSD x25-m
nVidia Quadro 580
OSX 10.6.3:
Dual Xeon 2.99Ghz
32GB ram
4 7200 disks in 4TB raid 0
Radeon HD 2600
Matrox MAX h.264 compressor card
Any advice on this situation would be greatly appreciated.  Thank you for your time
-Michael Emanuel

Hi Michael,
Sorry to hear you're having problems with Adobe Media Encoder.  I'd like to get some more information about the problem so I can better understand your workflow, and potentially try to recreate the problem.  For what it's worth, I often import files of different resolutions without any problem, so I want to find out what's different about how you're using AME.
Apologies for the long list of questions; the small details can be important.
-- After you import the first file, what else do you do in AME?  Change the preset?  Change the settings?  Change the output destination?
-- What are the properties of the files that are causing the problem?  You said it happens on "non-standard" files, but can you describe the specifications for one or more files that cause the problem?  Please include file type, length, frame rate, frame dimensions, field order (if applicable), alpha mode (if applicable), and audio type and rate.  If you know more the bitrate, both video and audio, that would be nice, too.
-- If any of the files are small enough, could you post a couple online that I could try on my machine?
-- How were these files generated?  What application created them?
-- Where are the files stored? A local drive, a network drive, a removeable drive (USB or Firewire), etc.?
-- Which Adobe application or suite do you have installed?  AME a limited set of options if you're using Flash or Web Premium compared to Master Collection, Production Premium, Premiere Pro, or After Effects.
-=TimK
-=Adobe Media Encoder QE

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