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
DAG size for ETC is 2.53GB which theoretically should make the 1060 3GB sufficient, however, if additional GPU memory allocation is required (e.g. by the OS) it just may push it over the limit.
Perhaps you want to try using the low intensity DAG (it is a checkbox in the miner settings) option in WinMiner. Cant say for sure that it will do the magic but it just might be the extra push to make it work...
When in "all coins" mode WinMiner will automatically avoid coins that can not be mined by the available hardware, and go for the right coin at any given time that is mineable by the available hardware.