I'm in the same boat. I'm avoiding the reinstalling phase as I have read in other threads that this DOES NOT work. Unless, someone else who had the same experience, says reinstalling with the instructions provided actually has been confirmed, I'm not going to go through that false hope.
I'm in 64-bit Logic, I want to move up to Logic Pro X (Where 32-bit Plug-ins do not work), and highly doubtful that Pod Farm will act any differently then it does on Logic 9.
My work-around to this issue is such a band-aid, it's not even funny. When I boot up Logic and open up a project, I stay the hell away from existing Pod Farm inserts. I can work with any of my Waves plug ins without any issues. If and ONLY if I have to go into Pod Farm, I save the file, go into Pod Farm, make my changes to the amp settings, and save the file again. After working with existing Pod Farm plug-ins, if I choose to open up another plug-in, I double-click, if the 1st double-click doesn't work, then I know something is wrong and I can predict that the next double-click will remove the plug-in. When it disappears, I go to Undo (The plug-in will come back to life), save the project, and exit out of Logic Pro all together. Re-load Logic Pro, and everything is back and running again (Again, avoiding Pod Farm plug-ins like the plague).
This band-aid takes a couple of minutes everytime it happens out of my schedule. So, I just avoid Pod Farm, and have moved to Amplitube with Recabinet impulses. I'm not bashing Pod Farm, I like the software and feel that the interface is the best out there, but something is off.
Hopefully, someone can confirm that Logic 9 or X with all of the proper unsinstallation procedures can say that it's works, I'll just deal with my above band-aid solution.