[quote user="Edward Averill"]
TMS320F28069 MCU, CCS5, XVS1000V2 debug probe.
[/quote]
Is it CCS 5.5?
[quote user="Edward Averill"]I'm noticing that, when I have breakpoints down inside an ISR, for 2-3 minutes I get the interrupts.. then they stop triggering. [/quote]
Is it possible that something may be happening to cause the program to no longer run correctly? Or is it that the program itself is running correctly, just the debugger is no longer stopping at breakpoints or updating variables?
Do you have some other means to debug the program? Maybe toggle a GPIO/LED instead the ISR and see if it works without the use of breakpoints etc.