The GPU issue happened to me even with the Setup version and Manual mode on.
Restarting the PC seems to at least stop the GPU if you uncheck the GPUs before it has the chance to start mining. The CPU doesn't seem to have problems but the GPUs just benchmarks a bit and then will stay on "idle" even though I can hear and feel it running.
Hope to at least hear from the team that they're addressing the issue, but hopefully they're collecting the data from our logs to solve this.
I found a similar issue although not related to WinMiner, I think? Mostly an issue with the miner. I decided to mine Ethereum Classic on my desktop computer with a RX 570 and 2 1060 3GB, but while the RX 570 mined Ethereum Classic just fine, the 1060 3GB GPUs didnt, WinMiner even downloaded several miners but eventually gave up and the GPUs remained actually idle, without mining.
Is it because of the amount of memory of my 1060 3GB cards? I wonder
Although I did see the same problem you are describing with earlier versions, I have not seen it happen to me with 1.109 yet. However I don't think the AI that decides if a card is appropriate to use with a particular miner or not is fully tweaked yet... I still see WinMiner try to mine with some very unsuitable cards, like a GeForce 8400 GS or even integrated nVidia chipset video. I'm sure they will get it perfected once they gather enough feedback.