Hit stop, wait a few seconds, hit start. Check on it every 15ish minutes. You might have to hit stop>start a few times. Mine is a pain in the ass also. Once it starts running it normally has no problems. After running one continent for a few hours it should have pretty much all of them downloaded, and it wont be a problem anymore. The hardest part for the bot during Archeology is the Downloading of Tiles, the loading is very easy. The debug tab will show you downloading Azeroth 34_02, loading Azer 34_02 or some other than Azeroth. Nothing you can do here but keep an eye on it for the first hour or so on new continents. After that it should run just fine
The problems I have seen, and I'll have to sift through my logs, is the timeouts of 30 seconds, and it not receiving anything back. I'm also not sure how it gets to the point, but it's show in the console log "No Data for Azeroth ##_##" a few times... Again I'll have to sift through my logs, but stop>starts got it working. Most likely this is because of my crap internet connection.
