I just came in here to post about that ;p
Its because I left an old subroutine in there that accessed ffmpeg.exe after i removed it from the package. I've reuploaded the package with the fixed exe file in it, and also added better error handling code to the runprocess subroutine so it will output the error to the log file if any files are missing in the future.
Just redownload the same link in the first post and all should be well.
The only thing I was still using ffmpeg for was to get the frame size and aspect ratios from files, but I found a much better/cleaner way to get that info using "Mplayer -identify -frames 0"
About the Aero thing, It seems like mplayer is causing that. Not sure why yet, but I'll try and find out if theres some way around that, but my dev machine is not windows7, so testing is a little harder for me. Its just a minor annoyance though, it doesn't effect the program functionally.
Update: Upon further research it appears it is the directx output driver for mplayer that causes aero to shutoff while mplayer is running. Try this version if you can and let me know if it still kicks you out of aero when encoding:
http://www.shinrasoft.com/amvbe/amvbe.exe I added -vo null to the mplayer -identify command which hopefully should fix that by causing it to not use an output driver at all to get the information about the file.