The place I'm working at has 3 Media 100s running v8.2.3, and 3 PCs which are used for encoding/ compressions.
In order to read/ compress Media 100 clips the 3 PC's are using the Media 100 Windows Transcoder dated 18th March 2004, which has been working fine for years. The last few days we've found that all 3 of the PCs are interpreting Media 100 files with the (slightly) wrong aspect ratio - when we open up a file which has been rendered to the Media 100 720PAL codec it is slightly stretched horizontally, and missing a strip from the far right. It's so subtle that you don't notice it unless you compare the output to the original - we discovered this because DVD overlays (rendered as still PSDs) were not lining up with DVD menus that had been rendered to the Media 100 codec (they did on a Mac, not on a PC).
It's definitely a codec/ quicktime issue - we eventually realised what was going wrong by comparing different codecs in After Effects. Everything works normally on a Mac (including non-Media100 Macs) just not on Windows machines.
This is happening on all 3 encoding PCs, on exports from at least 2 of our 3 Media 100s, but it only just started doing it...
The first thing i would check is square or non square pixel aspect ratio. Make sure you always use the 720 pal codec, there's a tiny difference with the 768 pal codec named Media 100 Pal codec used for analogic sources.