Now I see what you mean. In Mame 109 (and 072), it behaves exactly like you said. When the pitcher is aiming, up and down are reverse of what they should be. Pitching the ball seems to operate like it should. Switching the axes makes the pitching no longer work properly.
Were you able to play reasonably well in Mame 126u2? When I tried to play using Mame 126 or 127, the controls were really screwed up. For example, on the letter-choosing screen, I'm unable to home in on a particular letter because the cursor flutters around. In the older versions of Mame, this isn't a problem, and I can home in on particular letters very easily. Also, using 126 or 127, the controls within the game suffer from the same problems.