Hi,
Instrumenting functions for profiling changes their timing and also increases the stack footprint (the code that outputs profiling information takes extra time and requires non-trivial amounts of stack). Most likely, in your scenario this triggers a stack overflow, or makes the interrupt handler run longer than the period between the interrupts.
Unfortunately, there is no fully automated way to troubleshoot such issues. Our best advice would be to try excluding some functions from instrumentation, and to experiment with increasing the stack size and decreasing the complexity of the affected functions.