The logs show the video is supposed to be 256 lines for this game, and.... well you know what? I'm not surprised 256p won't draw every line on a consumer NTSC TV....
...
Maybe it really is as simple as that? The video mode will sync but there's no coaxing a consumer NTSC set to display 248 lines?
After all this - yes, I think so.
According to your 0.256 log, you are using this crt_range to allow 256p modes:
Monitor range 15625.00-16750.00,56.00-65.00,2.000,4.700,8.000,0.064,0.192,1.024,0,0,170,262,448,526
Which looks mostly like "generic_15", except the max/min lines numbers have been altered from default. I've highlighted them above. There are two sets of
min (red) and
max (blue), for
progressive and
interlaced respectively.
I suggest you to try the default NTSC crt_range, which is:
monitor "ntsc", "NTSC TV - 60 Hz/525", "4:3"
crt_range0 15734.26-15734.26, 59.94-59.94, 1.500, 4.700, 4.700, 0.191, 0.191, 0.953, 0, 0, 192, 240, 448, 480
If yours has been altered, you could always just replace your monitor.ini file with a fresh one from the download package. If you want to try further customisation to get 248p lines or whatever, try using NTSC preset as your base.
After you've updated monitor range presets, video modes and everything in VMMaker: go to "Edit Settings", then "MAME" (last tab), and be sure to tick the box marked "Export monitor settings to GroovyMAME". Then click "Browse" to make sure it is pointing to the right executable. Then click "OK" to update the mame.ini file.
If you do all this, you'll see a message in the VMMaker command window:
Exporting settings to mame.ini...
This will stop GM trying to display 256p modes on your TV. Unfortunately you may need to look at other options for those games (like using interlaced modes or stretching or somesuch).
I'm not sure why you still get lines cutoff even in some 240p modes. If the NTSC monitor range doesn't help, I'd look in TVs service menus.
Maybe being hopeful here, but I'd dive deeply and search through the TV service menu to see if there is an NTSC/PAL option somewhere. While looking, you might find something about screen size etc. Toshiba TVs around 2000 era (like yours alternative TV seems to be) all used these huge jungle chips with everything preloaded already, so maybe you just need to flip a bit. Many manufacturers at that time used Toshiba jungle chips, so they are fairly generic. I expect there to be up to 20 pages of settings, most of which might not be available unless you flip a special "PAGE" bit (it might be called something else) or even enter another code. Unfortunately some manufacturers for US market also might've tried to save a few cents by not bothering to put on something as simple as a PAL frequency crystal oscillator, so I might just be "dreaming". Anyway, worth a good look in the service menu to see what options are there.
Take care and exercise discretion with service menu options, setting the wrong thing can make the service menu inaccessible. It is possible to backup the TV EEPROM (which saves all the data) if you want to really get into it.
Sorry, this post has gotten long. From a practical perspective, looks like you are stuck with a snug 240p for now at least