Interesting. Support has said that this issue is also affecting 5.1 instances but they didn't provide any more info than that. It sure seems like this problem is hitting some people but not others and if you do get nailed with it, there's apparently no way to fix it.
Did you say that you had your 5-minute stats set up to Level 2 because of 3rd party app that access the database through the webservice SDK? If so, would you mind telling me which app that was?