I think 1 start would getting special VARS during the game would be a very good and easy sollution.
eg.
stage 1 gets var a=1;
stage 2 gets var a=2;
or var b=1;
On submit their should be a small function like
if(highscore greater then x && b!=0){
save new highscore
}else{
print(" you fooo tried HACKING us? huuu? hu? no its not ok! ur account just got BANNED entirly for life

}
?
:-)
edit:
Please make it actionscript 2.0 compatibel