debugging of interrupt bug - very annoying

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Hi All,

Setup : XMC 1300 + DAVE 4

I have one input from GPIO. I generate two PWMs, one when GPIO is high and the other when GPIO is low. I have connected both PWMs to their own counters. I then readout the counters via an interrupt acting on the GPIO pin rising and falling edge (different pin, externally shorted, thus same signal and confirmed on scope). I am trying to see of the counter counts correctly, but in debugging I only get nonsense.

I have attached my project.
How to use : Apply 100 Hz digital clock to both pins P0.12 and P2.4. Monitor pins P0.0 and P0.1 for PWM outputs.
What to see : PWM signals on P0.0 and P0.1 creates wavetrains of clocks, out of phase.
My issue : I am trying to count these super slow pulses with a counter from the interrupt, this just fails when I try and debug it.

Please help me understand how one can debug this.

Regards
Enigma
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