Very strange. Let's solve the first problem:
SainT use optimized CPU internal 16bits rendering routine (coz ATARI pictures are never greater than 16bits). Then, that buffer should be displayed on window screen, wich can be in 16 or 32 bits. If your windows screen is in 32bits mode, only GPU is used for 16 to 32bits conversion. Unfortunatly this is not supported on your video card in windowed mode ( looks strange for TNT2, did you install the lastest drivers ?).
To enable CPU rendering in windowed mode, just set your windows desktop to 16bits mode. so you can try the windowed mode on your config. ( Maybe I'll add a slow 16 to 32bits conversion routine for CPU only rendering in futur version)
Other important tips: SainT 1.99 could crash in a way the crash stay permanent ( because of a ROM overwrite ). I should fix that in the next version, but you can bypass that by clicking on the ROM file in the option file, and then click on "Set Active" button (even if the rom is already activated). This "force" SainT to reload the ROM file in its internal buffer, and may help to restore a previous big 68000 crash.
Let me know if it helps.