Hi ssalmon,
What’s the exact Jetpack release you are using?
Are you using PAA.00 as PPS source and try to control it manually?
If so, why you configure the same for PPS input?
If not, what’s your PPS source.
Please share the block diagram of your connection for further check.
You can also refer to the following topics for PPS porting:
PPS input to GPIO on Jetpack 6.1 - #8 by erik93
Pps_gpio interrupt not asserted - #8 by KevinFFF
Enable PPS on Jetson Linux 35.3.1 for Xavier AGX