Does the tool path look correct in Mach 3?
If it does and you're using CV mode and your accel could be too slow on one axis (but not the other) to keep up with your feed rate, Mach 3 will round the corners as it's trying to pick up speed to change directions while maintaining your feed rate. If this is indeed what's causing your troubles, you could try the "exact stop on angles greater than" setting and set it to perhaps 89 degrees and see if that fixes it.