Thanks for following up. Hmm, well I guess that's good that it is working now anyway.

If you happen to run into it again, please post the problem model.

My best guess is that there was some problem in the join process in the case where you ran into a problem - filleting won't work well if something went wrong with the join and edges that you thought were fused together really weren't attached to each other. A situation like that could fail to fillet kind of like you described.

- Michael