Embedded Linux board using a GPIO-PPS (without GPS, etc.) for time conditioning - ppstest can SEE the signal and report, but no time conditioning

Question

I'm attempting to condition time on a Xilinx ARM board. I have a PPS signal coming from another board (right now, just a desktop function generator providing a square pulse.) I'm using yocto to build this image:

• pps-gpio is enabled in the Linux kernel
• the device tree has a PPS node which specifies the GPIO the signal is attached to
• ppstest DOES recognize the signal and prints to the console:

[root@myboard /]$ ppstest /dev/pps0
trying PPS source "/dev/pps0"
found PPS source "/dev/pps0"
ok, found 1 source(s), now start fetching data...
source 0 - assert 1632177209.938875976, sequence: 407 - clear  0.000000000, sequence: 0
source 0 - assert 1632177210.941050397, sequence: 408 - clear  0.000000000, sequence: 0
source 0 - assert 1632177211.943125187, sequence: 409 - clear  0.000000000, sequence: 0
source 0 - assert 1632177212.945262438, sequence: 410 - clear  0.000000000, sequence: 0
time_pps_fetch() error -1 (Connection timed out)
source 0 - assert 1632177217.955604800, sequence: 411 - clear  0.000000000, sequence: 0
source 0 - assert 1632177218.957730860, sequence: 412 - clear  0.000000000, sequence: 0
source 0 - assert 1632177219.959654719, sequence: 413 - clear  0.000000000, sequence: 0
source 0 - assert 1632177220.961705029, sequence: 414 - clear  0.000000000, sequence: 0

(The Connection timed out message is where I turned the signal off to make sure it was indeed printing based on this signal, which shows it is using the correct GPIO)

However, if I modify the signal a little bit to try to speed/slow the clock, it doesn't work - the time stays at 1 Hz, instead of 1 Hz +/- a bit. I'm attempting to use chrony for the management of this:

refclock PPS /dev/pps0 lock NMEA refid PPS precision 1e-7

And tried running chronyd from the command line:

[root@myboard /]$ /usr/sbin/chronyd -f /etc/chrony/conf.d/pps.conf -n -d
2021-09-20T22:50:14Z chronyd version 3.2 starting (+CMDMON +NTP +REFCLOCK +RTC -PRIVDROP -SCFILTER -SECHASH -SIGND +ASYNCDNS -IPV6 -DEBUG)

I've run this as a background process while running a loop to print the time every second, and verifying the time with a stopwatch. I've tried raising and lowering the PPS signal a little faster and slower, but there's no change in the time, as verified by my stopwatch. How can I verify that this is actually doing anything? Are the changes I'm making too significant and maybe it's throwing the signal out? I'm not sure what to make of this exactly.