Hi outrunner,
You can easily see the resolution picked by GM in the Game Info submenu. If it's picking the right height, then the lines should be there.
Many "modern" TV chassis may do things like cropping lines above 240, etc., this is a known issue.
It could be, however, that GM is using interlaced resolutions for those games, and picking the highest possible height for the given refresh in order to provide better resolution. If that's the case, then it's a matter of reducing the InterlacedLinesMax value in a custom crt_range line.