When I play SCCT; I sometimes have to shut the game off to do something. But if I try to turn it back on it says the game is still running so I have to restart the computer to get back on. Is there anyway to fix that??

Did you actually exit the program all the way or just quit the Single Player section? Instead of re-powering off your computer you can also hit Ctrl/Alt/Del to see what processes you have running and close it from there.

I exit the program like normal (pause then hit the exit game button) and whenever I try to load it back up it says another instance is running. But it doesnt show up in the task manager.

There is something on your system that is preventing the game from shutting down properly - possibly your A/V or a permissions problem. Keep your system lean and run it in a selective startup - that will prevent background processes from running and conflicting with the game.

Start>RUN
in the RUN box type MSCONFIG

Under the general tab choose Selective Startup
uncheck the box that says 'load startup items'
Apply
OK

and restart your computer