This is pretty common. The problem is that the vertical games in question use 288 lines. Most horizontal games use ~240-256 lines, so when the screen is adjusted for these (horiz) games, the remaining (288-~256) lines are cut off.
You have a few options:
1) rotate your screen to suit each game (ideal but not usually practical)
2) Put up with vertical game top/bottoms being cut off (shame if you like vert. games)
3) Adjust so that vertical games fit, but put up with top/bottom borders on horiz. games (shame if you like horiz. games)
4) Use a non-native res. for the vertical games (not arcade perfect).
I personally go with no. 4, since my 'classics' are all horizontal. Plus I would rather see all of the (vert.) game and be able to play it and put up with a bit of non-authenticity. My 'ArcadeVGA M.A.M.E. Resolution Tool' allows you to setup resolutions like this easily (automatically in fact). Get it from my downloads page at
http://mamewah.mameworld.net 
Edit: Just thought I'd mention that I use 640x480 -hwstretch for said games =>256 lines.