[Alan Anderson]

The only difference in the GTS signal for the two directions is the length of the high-going pulse. It should trigger identically for both CW and CCW sensing. Unless you've forgotten to take out the "phase B" code, I can't think of any reason it would count in one direction but not the other.

Or maybe you're not properly accounting for the fact that you get both high-going and low-going interrupts on pins 3-6, though that doesn't seem to be likely to cause the results you're getting.