The setting "Kill miner and try again if mining hasn't started within 60 seconds" is enabled. I think what could be it in this case, is that the blank window isn't a cgminer.exe process at that moment. Eventhough it says cgminer.exe in the window title. All the other times I think it works fine I guess.
I managed to make screenshots this morning. The CGWatcher log stated: "cgminer closed outside of cgwatcher."
I downloaded CGwatcher 1.3.4.6 yesterday and my problem with the blank window hasn't occurred since. If it does occur again, I will try your test build.