Programming a Chronograph in C

I am having trouble programming a chronograph I made. I works fine but I want to be able to use it by shooting or dropping whatever through it from either direction, bidirectional. For some reason the code is hanging at the OR || operator I used in my while loops according to the debugger. Not sure what is going on. Anyone have suggestions as to get around it?

Line #86 and #91 are the problem http://pastebin.com/19M3800C

Thanks