"Disable internal geometry" means "use external geometry" (wait a sec!). Internal is the plugin's own super-leet-custom-hand-coded-for-n64-games-by-Jabo transforms engine, External is yer bog standard DirectX transforms engine. Internal is supposed to work all the time (it's got better with each version of PJ64) so you aren't "supposed" to need external in v1.5, but there might be places where you do (you seem to have found some) hence the option, plus it can be faster and allows Hardware TnL (DX7+). Yes using this option certainly will have a negative effect on some games, because DirectX transforms are not as accurate, but there are exceptions. So er.. all i can say is keep this off except where you find it definately helps. As for the TNT2... to be honest i'm not totally sure if that's related, brain isn't working ATM... maybe i'll get back to you on that.
