Hello,
Hmm so from uC point the ISR is working properly.
Only in the debug mode you have issues.
Did you try to set breakpoint to ISR and run the code from reset Did it reach the ISR?
For any setting withing debugger please contact debugger vendor, maybe there is something. But I have personally never encounter such issues on multiple debuggers.
This whole issue seems strange. Please share with me code which demonstrate the issue.
Best regards,
Peter