WowAce

What steps will reproduce the problem?
1.  Open gathermate options
2.  Run database maintenance/cleanup
3.   Game will complety freeze up.  After a few minutes, I wil eventually get a disonnected from server error.

What is the expected output? What do you see instead?

before MoP, there would be a long game freeze, but eventually it would return with extra nodes removed.

What version of the product are you using?

1.22

Do you have an error log of what happened?

no logs are generated

I took a peak at your cleanup code, and the way you search for nodes as a loop within a loop within a loop is perfectly fine – in a multithreaded environment.  Unfortunately, Blizz treats add-ons as singlethreaded, so if anything runs for a long time, it locks everything else out.  If the servers don't hear back from the clinet within a few minutes, it drops your connection  In researching this, the way you’ll probably want to fix this is to break up the GatherMate:CleanupDB()  function into a coroutine.

Not all of us are blessed with super high-end machines.   My gatermate2.lua savedvariables file has 59,000+ nodes in it.  thats ALOT of data to sift throguh. I saw someone wrote up a similar ticekt that marked invalid for some reason.  He's probably having the exact same problem as I am.