Audio question on mkvtoavi, if Encode DTS to AC3 is left unchecked, is this likely to lead to audio being out of sync?

I converted an mkv (h264 and dts streams), left Encode DTS to AC3 unchecked and the output audio was at least a second out of sync.

Hi, in addition to the above, I have re-tried the encode and when leaving the encode dts to ac3 checked, the audio is no longer out of sync.

However, I'm trying to insert my new .avi into Sony Vegas Pro, but it will only pick up the video portion, and leaves the sound out as it cant detect it?? This must be the reason why when I put it into usb and plug it into my blu ray it wont work.

Please help this is a nightmare!

Unfortunately the only bit of my log ive saved is

eac3to v2.72
command line: "D:\Dan's Misc\mkv2avi\tools\eac3to.exe" "D:\Dan's Misc\mkv2avi\tools\Twilight Saga New Moon-srcaudio2.dts" "D:\Dan's Misc\mkv2avi\tools\Twilight Saga New Moon-srcaudio.ac3" -448
------------------------------------------------------------------------------
DTS, 5.1 channels, 2:10:39, 24 bits, 1536kbps, 48khz
The ArcSoft and Sonic decoders don't seem to work, will use libav instead.
Decoding with libav/ffmpeg...
Remapping channels...
Reducing depth from 64 to 24 bits...
Encoding AC3 <448kbps> with libAften...
Loading white noise (needed for dithering)...
Creating file "D:\Dan's Misc\mkv2avi\tools\Twilight Saga New Moon-srcaudio.ac3"...
eac3to processing took 5 minutes, 7 seconds.
Done.