If you haven't already, I'd suggest reviewing the PGP Release Notes for any known conflicts your sytem may have with PGP. If you don't have the most recent version of PGP and you are eligible for a free update, I'd suggest you give it a try.
I'm guessing that you have actually encrypted your disk. If so, you may want to decrypt it to see if your normal update functioning occurs. I mention this because there is always the possibliity that using PGP and this update problem may be just a coincidence - I've had several experiences when I've made some change in my computer, suddenly had a problem, and incorrectly concluded that my change had caused the problem.
If the problem still continues, I'd then try uninstalling PGP (having first decrypted the disk) to see if the PGP installation itself is actually causing the problem.