Nah, not my system or the rendered files, I run a tight ship over here!
Anime Sudio simply chokes on the large files. I rendered the project four times and different files were missing each time, but I was able to combine them into one good movie in After Effects.

Thanks for the reply. Quicktime was giving me trouble (has to be manipulated with bones and they weren't working very well in the scenario).

File names are good: cat001.png as an example.

No moved images, though they are outside of the Anime project's folder, I didn't think that mattered though?

Very strange problem, but very consistent. Doing a short 200 frame animation with three image switch folders, each having from 100-200 frames in them. Anime Studio Pro will just randomly replace them with the dreaded broken image icon, even when rendering. Ugh. It's an HD project, so maybe it's chok...

Also the compression method for the DVD could be a factor. MPEG2 makes its own "intra frames" and parts of the shot that don't move are combined with the adjoining frames.

You could convert part of the DVD with mpeg streamclip to Quicktime Animation codec or similar, then go frame by frame.

A couple little things for you. If you're doing an NTSC project you should work in AS at 720x540 (square pixel resolution) then make your project non-square tv ratio in FCP (720x480 or 720x486). Render out of AS with Anim Codec set to 90% or high with same frame rate as your project. In FCP, if you ...

I had a massive computer failure so lost this program and had to dig to find it again. This should totally be a sticky topic. It has some really handy features for large projects. Just my 2 c.