Teensy, probably a bad choice?

[Deleted user]

https://forum.pjrc.com/threads/41857-Options-for-bare-metal-development/page5

If I were you, I would look at the LPC branch of GRBL. It doesn't use a 2nd timer to control the step signal delay required by many stepper drivers (but rather, uses a delay in the stepper interrupt itself to implement the small delay required, that intelligently makes use of the time used by any calculations [code-time] of the ISR itself)...

One less timer needed may solve your issue, that I see has been ignored by the fairly rubbish Teeny support staff on page 5 of that link. You will have to read the current timer value and subtract it from the reload value (and perform a full timer reset - which isn't accurate at all, really) but that's the price for using a Teensy.

(Teensy simply isn't a great product. Lots of I/O, but far too many hardware bugs to work-around... and I'm pretty sure I hit most of them, wasting too much time, for my continued support).