I've been having the same problem with version 10.0.2.built 13. After doing a lot of root cause analysis (for about a year now), I think I've narrowed it down to our weekly McAfee AV update. Through process of elimination, it finally became clear that the vast majority of our helpdesk calls reporting this problem were coming in on Thursday mornings. After several months of this trend, it was beyond coincidence that the only vector was this update. The only deviation from this trend what when the user's computer was either shut off or literally off site (i.e. laptop) and was updated upon first opportunity.
What has made this issue impossible to nail down is because it would only happen to about 20-30 users out of the 7,500 user install base. It never happened to the same user twice or if it did, the time span between incidents was so long, it went unnoticed. There are no errors in any of the logs or even any indications that any kind of a fault has occurred. It's almost like the PGP service has been shut down but not fully restarted (or something like that).
We've only come up with two work-arounds... Stop/Restart the PGPSERV service and restart PGP Desktop, or simply reboot. As I mentioned, it doesn't happen again after that. The bottom line is, I can't prove a darned thing other than the fact that I need to upgrade my Universal server and update about 8,000 laptops and desktops.