I'm pretty sure its not an issue with the contacts because I always clean any and all carts thoroughly for the very same reason you list. Makes my friends wonder about my cleaning brand new carts!
Admittedly I didn't try it in the 6 slot because I was testing some other carts as well with the MV-1 (Metal Slug X and KOF 97) and after and extended testing session I had to run some errands.
I will see about trying it in the 6 slot this weekend. I expect the results to be the same as with ROTD. Issues playing in the 1 slot, but plays perfectly in the 6 slot. I guess I could try cleaning the MV-1 board but it has played MSX, KOF 97, KOF 2000, MOTW, and Puzzle Bobble flawlessly.
It seems likely its just the issues that the MV-1X models of the MVS boards seem to have with newer MVS carts.
Other folks have reported that the MV-1C plays MS5 just fine. Not sure about the MV-1F because I don't own that model board.