I just tried the trial version of Magix Movie Edit Pro 2013 Plus, and it seems to take UT-Video-encoded .avi files just fine; so it's probably not a problem with the new version.
Maybe the problem is introduced when reading the original file; which affects everything else downstream in the process:
Make sure CCCP
is installed so that directshowsource has the codecs necessary for decoding the original footage;
And if you are using ffvideosource, make sure you have the AVSPluginPack.exe installed so that you actually have ffvideosource to use as well.
(comes along in the AMVApp.zip
after you right-click and extract the files)
Or perhaps the problem is in the conversion process:
The UT Video Codec should be installed, and ULY0 should be selected and applied: Video > Compression > ULY0
After changing your sourcecall to ffvideosource, be sure to refresh the new script: Hit F5 on your keyboard.
(If you open the .avs script with Notepad, you should see what sourcecall is actually being used.)
Check the UT-Video-encoded .avi file in Media Player Classic to see if the problem is present there too.
(MPC comes with CCCP.)
Other than that, maybe disable the audio stream in VirtualDub: Audio > Disable
(It's usually best to treat A/V separate instead of multiplexing the audio with the video)
Hope this helps