I too have this problem. It's been happening for years now.
For some reason, earlier around iOs3 I believe, you could unplug your idevice at the back up stage of syncing and that would lower and fix the "other files" problem.
Since iOs4, you haven't been able to do that. It is SO annoying!
I am now up to 1.25 G of "other files" and I wish I could get rid of them so I could use the memory for videos!
I wish someone would fix it but I guess we're outta luck.
Restoring used to work as well, I did that last night, it didn't help any longer.
I think I figured it out. The other files grows when I delete videos from within the iPad instead of letting a sync delete videos I am done with. Its almost as if they dont delete everything. But when I see that other file getting big I simply power off my iPad and then power it back on and that space is cleared up.