Had the same problem with other game (SNES version is TASed, I know):
http://youtu.be/tFLPJVZu0sM
Someone told to download Sega CD .cue Maker, but I had XP then and to open the programme I had to replace comdgl32.ocx file in the system folder and I gave up:
http://softadvice.informer.com/Sega_Cd_Cue_Maker.html
I don't know how it works on Win 7/8, so you can try it. I read that foobar2000, CUE tools and xrecode II had .cue making function, so you can try 'em too.
EDIT:
This is a quote from a SonicCD submission:
"This movie happens to stay synchronized regardless of whether "Perfect SegaCD Synchro" is on, so if SegaCD emulation is chuggy on your computer, it might help to turn that option off for this movie. It would also help to use BIN+CUE instead of ISO+MP3, because it takes more processing power to decode MP3s than to not decode them.
Desync Issues
If you're getting desyncs, first make sure you're using the correct ROM and BIOS and emulator version and settings as described above. And don't try to load a mounted disc with "Boot CD", just use Open ROM on the file like normal.
Also make sure you have the right number of audio tracks on the CD... if you're using a cue file that means your cue file needs to have the right number of correctly indexed audio track sections, if you're using MP3s that means you need exactly 34 MP3s named properly and in the same directory as your ISO (if the ISO is "Sonic CD (U).iso" then the MP3s should be "Sonic CD (U) 02.mp3" through "Sonic CD (U) 35.mp3"). The actual contents of the audio tracks can be almost anything, but the number of audio tracks has to be correct otherwise the emulated loading times will be different enough to cause a desync.
Music
This was made with the US version of the game, but if you prefer the music from the Japanese version, you can tell Gens to run the US game but use the music from the Japanese game. The way of doing this depends on whether you are using ISO+MP3 or BIN+CUE. If you are using MP3s, simply replace the MP3 files with the ones from the Japanese version. If you are using BIN+CUE, you can edit the CUE file of the (J) version to use the (U) version for track 01 (data) and use the (J) version starting at track 02 (audio). It should look like this, except with the filenames matching the ones you have:
FILE "Sonic CD (U).iso" BINARY
TRACK 01 MODE1/2352
INDEX 01 00:00:00
FILE "Sonic CD (J).iso" BINARY
TRACK 02 AUDIO
PREGAP 00:02:00
INDEX 01 12:14:49
TRACK 03 AUDIO
INDEX 00 12:18:63
INDEX 01 12:20:63
TRACK 04 AUDIO
...and so on...
One thing those won't work for, though, is the ending music. For that, you'll have to use the actual Japanese version of the game, not only the Japanese audio tracks. You'll also have to use a different version of the movie file for it to sync and version 1.00 of the Japanese MegaCD BIOS. Be warned that Quartz Quadrant has slightly slower in-game times than in the US version (differences during lag frames) even though the movie is about 10 seconds shorter (mostly due to shorter level end music)."
I think this is useful information!
