Ok, I set up a dummy hydrus and got all the repository files, I merged them into the main ones files, and am going thought the relatively painfully slow process of processing them, it seems to do just fine for 3-4 then drags to an absolute crawl, not sure if this is just a visual bug or whatever.
to check if this was going slower because of the client size, I restarted with nothing, and it was about the same, however I paused all network traffic and repository synchronization.
I unpaused synchronization and it didn't start up, I had to manually tell it to start processing.
so what I found was pausing all network traffic paused repository processing, my use of pausing all network traffic was just to kill anything from downloading when I didn't want it to, if its meant to also pause repository processing, I suggest changing its name, if its not mean to pause anything downloaded from being processed, there may be some code tangled in that, I suspect that it also wont let other processing happen automatically, but don't know a good way to go about testing that or even know all of the background crap that may go on in idle to begin checking everything.