Thanks for the response.
With this code, I am moving the wheel very slowly so I can see the interrupts and what values the intflags have. I know that when I actually start spinning the wheel quickly that portion will have to be taken out of the interrupt handler. There is a section of code in the mainloop to display the counters and elapsed time, that is diabled so that the display from the actual interrupt subroutine is long enough to be able to read it.
In the final version (assuming I can solve this problem, the max rpm will be 100-150 RPM