To look at all this code for one issue without being able to test it and not having a clue where this one issue is and what most of the variables are or do is asking far too much!
Before continuing any further you first need to look at this and think... surely this could be optimized? If you've got a lot of repeat code then it definitely can be optimized. All this code can be shrunk down a ton via functions and arrays.
So let's dissect this...
So... explain what's going on here and what the variable C1R1 is and relates to?
Quote: "If C1R1=0 and timer()-GameTimer >400 then C1R1=1 : GameTimer=timer()"
Also you do a lot of repeat checks, for instance, if the mouse is at a certain position over I'm guessing a button then it can't be over any other button so it's not necessary to check that. So you need a way of checking until over a button becomes valid and not check again.
"Get in the Van!" - Van B