Hi Scott,
There are a couple of things that could cause 01 to be appended to the filenames. The first place to check is Photo Mechanic's Files preferences. The Renaming method menu has an option to always append 01, 02, 03 etc. See the attached screen shot for this option. Just select the top option to Append a letter when needed (A, B, C).
The other possible cause of the 01 getting appended to the filenames would be if there was a second line in the Rename field with 01 in it. Just click in the Rename field, select all with Command-a and then hit the Delete key. Now type in the variables. Most people that report this issue have copied and pasted text in the field, which included a carriage return at the end of the line and possibly 01 on the next line.
Best regards,
--Bob