I bet that the games that are cut off are probably all vertical games that uses 288 display lines (on a horizontal monitor).
In that case a tradeoff needs to be done. You can run them at 15k resolutions with 288 lines and a 51hz refresh rates and the games will run slower than original (if you use vsync or tripplebuffer) without being cut off OR it will run at 60hz refresh rate (original speed) but with only 240 lines and they will be cut off.
I didnt use much the Gavin Benson tool, but in the mame resolution tools you can tweak the "match refresh rate..." and "match resolution..." in the video mode selection menu. Alternatively you can select manualy the mode for those games to make it like you want.
If either of both option above doesnt fit your needs, you can try running these games at a 25K medium resolutions, they will not be cut off and will run at the original refresh rate but the display will be smaller with black border (ie, the game will not fill the screen). You must have installed the Ultimarc Trisync utilities to use resolution above standard.
hope it helps.