The OP's problem is not due to the nature of the reflected IR but with the behavior of the lm 393 comparator ( used in the circuit without feedback )which is processing the signal from the IR receiver photo transistor.
This is for a turning shaft with a dark or light spot to detect, as opposed to a magnet?
Why the comparator? Just use the detector as a switch to ground the pin or not. Choke the view with an aperture if need be.
At full speed this is the one that takes 41usecs to turn 1 degree? How wide is the mark? You should be able to catch that every time just polling the sensor with a 1 degree wide mark. Even port reading up to 8 sensors you shouldn't miss it passing any of them at least if you write clean non-blocking code.
Interrupts have an overhead that can trip you up. Attaching and detaching just makes it trickier.