Compressor 4 Changing my video length

I'm creating digital signage files using Motion and then exporting the file as a .mov file. When I use Compressor 4 to convert the .mov files to .mpeg 2 files, the length is changed in the video either adding black to the end or cutting the video off before it is finished. I've used older version of Compressor and never had this problem. I'm guessing there is a setting to be changed somewhere to fix this, but can't seem to find the solution. Any help would be very appreciated.

This is very strange, but I'll explain and see if it means anything as to why this is happening. I just bought a new iMac and bought new applications and the whole works. The new machine is where this timing problem is happening between Motion and Compressor.
I have a 3yr old Macbook Pro with my older applications that has worked fine for years.
In my frustration just now, I was taking my .mov files that were exported on the new iMac to older Macbook Pro to use compressor on that machine - assuming that would solve the problem. It did solve the problem, but I discovered that the files I was working with play differently on each machine.
There are two files. One is a 30 second mpeg and the other is a 45 second mpeg. On the Macbook Pro, they play just as they are supposed to. On the new iMac, the 30 second file stops at 27 seconds and the 45 second file plays for 1:30 showing black after the initial 45 seconds.
Does that make any sense at all? I'm stumped. Both files were built, exported and compressed the very same way.
Thanks again for any insight.

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