Converting MOV to MP2 mux error

[Compufix]

We need to convert a DV MOV file exported from Final Cut Pro as a DV NTSC Self contained movie file (we have done this NUMEROUS times). The video format is MPEG2 (FFMPEG) 352x240 @ 900 kbps. Audio is MP2, Options has High Quality selected.

Normally this encodes the asset and MUX happens as it should, resulting in the mpg file that we then import into our IP video system. We upgraded our towers to new Mac Pro systems running 10.6.4 (was running 10.5 and 10.4.11 on 2 different towers) and this process has worked flawlessly for years. Now, when we encode the files we get the separate audio and video files, but the MUX fails with a underrun error. It has happened repeatedly. If I go into the TOOLS tab and manually MUX the resulting files, it works and the resulting file is fine.

Any thoughts?

[Compufix]

As a side note, when I skip the SUMMARY screen, choose VIDEO select MPEG2 (ffmpeg) then open the file I want to convert, in the SUMMARY window, it shows unknown source format. But, if I drag and drop the file into the SUMMARY window, it sees it as a MOV file with no issues. I just re-tested and sure enough, it worked.

[Vampire74]

I believe I have a similar problem.
I need to convert a DV file into a MPG. However I don't get a separate audio file! I need a stand alone MPEG-2 file. ffmpegX doesn't seem to want to merge the audio & video files.
I tried to merge both files in Quicktime but then I get out of sync audio.
I need to play it on a similar system.