IMHO I haven't had to use a PAL mode in I can't even remember how long. I guess for some old games and such, but WHDLoad takes care of that. Are you sure your monitor supports 50Hz screenmodes?
I don't understand the other questions you're asking. Maybe the card is overheating, or not seated properly? Many users install a fan if using a desktop A1200 chassis. Do a google image search for ideas on fan mounting.
The config tool for the AGA version is a lot more fussy than the ECS version, but have you tried fiddling with that?