You can confirm that your settings are correct in the right-hand pane before you perform the rename. Does everything look OK there?
Yes looks fine, it's very strange though seems to be working ok now. Before its was like it gave up applying any tag changes resulting from the rename,move copy files tool. The first time i tried i didn't realise you can tick filename and set the rule [Artist]_[Name] so i had tried to set that bit in the place that you add rules for folders so i had put all this in one box: [Grouping]\[Publisher]\[Album]\[Artist]_[Name]
i wonder if that had made it stop working properly. I also had auto import running in the background. I later corrected those things but still seemed to be having the problems...
I'm not 100% sure its solved but seems to working ok for the moment
UPDATE: I'm sure this was just because i was learning the feature at the time. I've been using that feature ever since now and everything's fine