It's an issue with the individual gear ratios, they don't actually change no matter what you set them as. Final drive and the automatic top speed adjustement do work properly, but of course some cars have big gaps for no reason so they're screwed up.
I'm pretty sure the problem affects all cars, and both the manual and racing fully customisable transmissions.
EDIT: If you set all the individual ratios to something stupidly short (like 80 kmh in 7th in the Tomahawk), even without touching the automatic adjustement or the final drive it'll actually work.