drivetrain protection...

I REALLY need help with this...I went to go get my computer flashed back to stock today..and for some reason the car feels like it has some kind of drivetrain protection shit...i cannot have the clutch in and rev my car past 2200 RPMS...if I take the clutch out I can rev it as high as I want all day long...when im driving it..and in gear but w/ the clutch depressed..i cannot rev it high..only to 2200 RPMS...when the car is in neutral..and I let off the clutch..i can rev it as high as I want...what the hell can I do to fix this..its very aggravating and embarrasing because it makes me look like I cant shift.

also whenever i take off fast or something..when I shift..it kills the timing then when its gets to a low enough RPM it jumps me back and jerks the car..