Compressor making problem Program Stream Mpeg2s?

I'm having an ongoing discussion with the manufacturer of our video playback server (Leightronix Nexus) at our station. The box uses Mpeg2 Program Streams for playback.
I have Compressor 3.0.2. The Nexus playback is having occasional stutter problems playing back the Mpeg2 fies created by Compressor. I've verified bitrate, compressor settings, reimported the original footage, etc, but nothing seems to help. Finally I got a response back from Leightronix that reads:
"The problem is Compressor is not very good at creating a MPEG-2 Program stream file. Use ffmpegX to convert your MPEG-2 transport stream from Compressor to a MPEG-2 Program stream that will play fine on the NEXUS."
I'm trying to get additional technical information from them on exactly what Compressor is or is not doing, but I'd thought I'd ask first if anyone else has had issues with the Mpeg2 PS output from Compressor for anything they're doing? All these files play fine on the Mac itself, it's just when they actually air for us.
Kris

Further information about this problem ... the issue is that Compressor is creating a VBR file which has some problems. In portions of the video where there is a mostly white background or mostly black background (say a white screen with a single word of text), and creating an Mpeg2 Program Stream with VBR (6 min, 7.2 max), the algorithm will cause the bitrate to go way below the minimum during that portion of the file. Quicktime will play it correctly but other playback machines have a problem with it.
We were able to get around the problem by just setting Compressor to CBR @ 7.2 but it's still an issue. If anyone at Apple wants a copy of the Quicktime MOV we were converting, contact me at [email protected] and I'll get it to you.
Kris

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