Double digit seasons

I'm having a problem with shows that have 10+ seasons. The folder/files for the 10th season (and above) are formatted exactly the same as the first 9 (for example Frasier - 1001 - The Ring Cycle) but they aren't found during a scan. Moreover, when I manually tell it where the file is and save, it doesn't keep this change after saving. I'm sure this is something simple I'm missing since a lot of shows have 10+ seasons.

Thanks in advance.

Edit: other problem fixed

one problem is that 4 digit episodes are so near a year 2011 it is hard to tell them apart. a sure way is just to edit the shows

1011 to s10e11 before running tvrename. If you have shows like aaz-showname.s00eoo you need to edit the aaz- off the front to get tvrename to work on them also.