"Shouldn't" and "Isn't" are too very different things.

If one set of files doesn't work, then there's something different about those files. It could be that your tagging program is doing something different *because* of the difference in those files, and while the difference itself wasn't enough to make Rockbox crash, once the tagging program does its different things too, that causes the failure.
Just a possibility.
Of course, if you made all the files yourself, this wouldn't be a problem.