The problem appears to be resolved on all of our servers that were experiencing it. It looks like the Auto Protect File Cache was at the root of it. Turning off Rescan cache when new definitions load appears to have fixed things.
http://www.symantec.com/business/support/index?page=content&id=TECH210603
I was initially concerned about turning this off because it seems like this would leave stale whitelisted items in the cache. But the following article indicates that if the rescan option is off, the cache is cleared when new definitions arrive.
http://www.symantec.com/business/support/index?page=content&id=TECH191600
In our case, I suspect that either there was corruption in the cache and the side effect of the cache being cleared fixed it, or the option itself is suspect and is better left off.