Yeah you have to be careful with UPX4PPC, I'd first recommend downloading the latest version from here:
http://mobile-sg.com/software/?p=UPX4PPC&platform=ppc
Although you may want to do it after decomprssing your files.
I don't know which ones affect PIE. And I know there's a specific one for WP that cannot be UPX'd but can't remember which one... if you run a search you'll find it, I remember it was posted by Malatesta.