Hello JackWhite,
This probebly is becouse of the security that has been buildin PT2k5, some registry-key's can couse problems when removed.
Also, check if you have the 'Deep' scan mode selected. This can improve the results.
There is an other option 'Don't show items that would be automatically re-created', which filters key's that are incorrect/obsolete, but would be re-created after removal or after a reboot.
Check those options out, and mabye it will improve the result. But it is only for your safty that it doesn't remove everything, that could be wrong.