Hi Naresh,
I hope you've declared a and b globally as int16 datatype.
I too check the same on my C2000 launchpad:
Uint16 x=4,y=2,a=0,b=0; //In main added the following lines if(x>y) { a=1; b=2; }
Here are the screenshots of the Watch window before Free Run and after Free Run:
So, I don't think there should be any kind of skipping as you're experiencing.
Regards,
Gautam