Tomato can't load video

For some reason, whenever I open a wmv file for tomato tracking, it gets stretched absurdly long, and no other formats work. Anyone know what’s going on? FFMPEG issues?

“no other formats work”? That’s simply untrue. I would suggest you don’t include such baseless claims in your requests for help.

Don’t use wmv. It’s a closed format designed for streaming video on the web. I don’t know what the specific issue is that you’re experiencing, but wmv is certainly not an appropriate format for this sort of work.

So far I’ve had success with the MJPEG AVIs, and as always image sequences are the most stable and reliable way to go.

Well, I tried converting the wmv into mp4s and avis in Pitivi video editor, but those don’t even show up in the file browser.

Don’t use mp4s either. Avoid all compressed, streaming formats.
If you are having troubles converting with Pitivi, then contact them or use a different tool.
Personally I use ffmpeg.

But I thought FFMPEG doesn’t work with Blender. I purposely avoided it when converting the video into other formats.

You’re getting a bit mixed up. FFmpeg is a program that can be used to transcode media. It also provides libraries that can be used by other programs. VLC uses it and so does Blender (although as you’ve probably read there have been issues recently). It’s command line, so I wouldn’t suggest you directly use it unless you’re willing to do some reading.
Try VLC maybe, or avidemux.