Here is one more possible error: 32bit mp4 files have a filesize limit of 4GB. So, if your conversion is bigger than that, you have to add a parameter to the command in the profiles.ini. Add "-4" to the command of the profile. It should look like this:
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[MP4 HQ (*.mp4)]
command=-e x264 -q 20.0 -d -a 1 -E faac -B 160 -6 6ch -R 48 -D 0.0 -f mp4 -4 --strict-anamorphic --decomb -m -x cabac=0:ref=2:me=umh:bframes=0:weightp=0:8x8dct=0:trellis=0:subme=6
This parameter will create a 64bit mp4 file but will break compatibility with iPod and/or PS3 (I didn't check this on PS3 though).
Hope, this will fix it for you...
Or do you get the error also on small testfiles?