I don't know if you've already found the solution to this problem, but I came across your thread while looking a faster way to convert these files, maybe a bulk method of some sort. I thought about writing an applescript to do it, but I haven't as of yet.
Anyway, if you download dumpster, you can open your individual .mov files, then go to the property called "nsav", there you'll see two fields, more than likely the second field will be set to $0001. Change it to $0000, and then save the file. For some reason, I always have to click out of that field before saving the file, otherwise the change doesnt seem to save.

Once you've done this, then you can run the .mov through any converter like VisualHub, and do pretty much anything you want with it.

The downside is that you have to do one video at a time. If anyone knows of a faster way to convert them, please post.

Hope it helps,
Woody