Hi Alex,
Thanks for the code snippet.
Have you also set-up the continous read synchronization in the setup() portion of the code?:
REG_TC3_READREQ = TC_READREQ_RCONT | // Enable a continuous read request
TC_READREQ_ADDR(0x10); // Offset of the 8 bit COUNT register
while (TC3->COUNT8.STATUS.bit.SYNCBUSY); // Wait for (read) synchronization
Might I ask how you're using or calling the micros2() function in your attachInterrupt()'s callback function?
Kind regards,
Martin