Haven't heard of that, maybe somebody else has? I suspect it will be fine, but I'd use the PCIe x1 slot. There wouldn't be any advantage using the x16 slot as it won't run any faster in that slot, and using that slot would prevent it being used if you ever did get a PCIe x16 card for something else.
I hope a new card fixes the problems, but there's no guarantee that it will. Cross your fingers but be prepared for more hair-pulling.