I get a higher FPS on Flight Simulator than CIT. MTA is just very single thread depended.Since when do you have lower fps? Did you restart your PC?
Idk if this gonna help in anyway but ... yesterday I re-installed mta with same resolution same settings , it got fixed for a bit but when I quit the game after some time and launched it it cameback like it was.
Sounds like a thermal throttling issue to me, open up your gpu and cpu temperature monitoring software (Example: HWmonitor), play MTA for some time, check your avg temps on them.