Ok, tried hle mode as you suggested but it didn't help. There is still a huge wait before entering and exiting the start race options screen.
To give more detail, i find the race i want to do, hit go, then i get a black screen for over a minute before i get to the start race, replay, settings menu screen. I get the same waiting time when exiting that screen after the race is over and i go back to the home screen.
Like i said, the same .bin file works fine with epsxe, so i guess fpse must have an intrinsic incompatibility with this game. I'm using the simulation disc btw, not the arcade disc if that makes any difference.