If -switchres is disabled, mame should be seeing that the monitor is rotated, and rotate correctly. "should"
Could you run mame from the commandline, with the "-v" option (or enable verbose in mame.ini)? Run it for both a correct oriented and a sideways game, and post the outputs here. (if you're using mameUI, you'll have to redirect the output to a file: "mameUI32 1943 -v > textfilename.txt", including the greater than sign that didn't bold very well on my browser.)
FWIW, mame had a simular problem with Intel on board video chips, where the video driver would automatically "rotate" the screen, so some games were sideways. I never heard it for an nvidia card, though. Which is why I'd like to see the verbose output to see if it's the same.