Basically it looks like the query is taking so long it's actually losing it's MySQL connection. The server load going up kind of goes along with it. Unfortunately there's not a real solution for this. How often do you have the cronjob running?
We've totally gone away from this model for version 7 because that was one of the downsides of the old method, is if you're board was decent sized the subscriptions scripts were very inefficient.
