I think we may need a bit more information, and a simpler example - ideally using just Arduino and Teensyduino.
I'd recommend you try with Teensyduino 1.59 beta 3, because there were some definite issues with bad interactions between the SPI and...
OK, I can confirm that installing the 0.59.3 board package fixed the issue. Thank you so much h4yn0nnym0u5e!
I will take the repo private for some time while I work on the project, then I will make it public again when it is finished. If anyone...