Are you certain that you're using the Recommended BBMpeg Settings as shown in this thread:
http://www.kvcd.net/forum/viewtopic.php?t=2224 ? Also make sure that you're selecting the correct .m1v (video file created by TMPG) and .mp2 audio file (created by Headac3he) for muxing, and not accidentally selecting one of your short Sampler encodes created during File-Size Prediction. Other than that, I don't know why it wouldn't be working for you...very
rarely you may come across a problem file that just doesn't want to mux properly with BBMpeg, but I doubt this is the case. Do you have enough free space on your hard-drive for the muxed output file?
As a last resort, if BBMpeg just doesn't want to mux this file properly for you, and you're
sure that you're doing everything right, then you might want to give TMPG's muxer a try. It's under File -> MPEG Tools. In the Simple-Multiplex Tab, choose
MPEG-1 Video-CD (non-standard). Then select your video and audio inputs, and mux. BBMpeg is regarded as a better muxer than TMPG and produces more player-compliant files than TMPG...this is why it's best to use BBMpeg (in addition to the fact that you can mux from an exact Start and End point with it).
Good luck,
-d&c