Hi Aaron,
In the Reg Cleaner Advanced options tab, is the box next to "Don't show items that would be automatically re-created" unchecked? If so, check it and see if it makes a difference.
If it makes no difference, try this -- maybe we can make some progress in figuring what is happening:
1. On the Reg Cleaner list, check just one of the lines that keep reappearing.
2. Right click on that line and select "Open in RegEdit" (did it open at the selected key/entry name/value -- if no, what did happen?).
3. Copy and paste into a new txt file these four items from the top of the Reg Cleaner window: Key, Entry's name, Value, Error Description -- then save it.
4. Click the Reg Cleaner Remove button.
5. Select the regedit window from the task bar and press the F5 key.
6. If regedit is still at the selected key/entry name/value, then Reg Cleaner did not remove it.
7. If the key/entry name/value (or part of it) is gone, close Reg Cleaner and close PT 2006, but leave the regedit window open for a while -- it should be positioned just above, just below, or at the same key depending on the type of item.
8. Now and then, select the regedit window from the task bar and press the F5 key. Does the item reappear in regedit?
Post what you observed and include the four lines you saved previously in step 3.