Hi CAlex,
Can share with me your project design?
Btw, I cant be sure this is related to the linuxsocfpga real time limitation or not, probably you can increase the time where your code detect an interrrupt triggerd to perform signal toggling. This will help to troubleshoot the running code because looks like for every 25us when an interrupt occured due to clock edge change and the linux application code must perform a signal toggling.
Another method is use a baremetal application to test your test code as a comparison.
I saw this document which talks about the latency issue:
https://www.rocketboards.org/foswiki/pub/Documentation/AlteraSoCLTSIRTKernel/ELC-Linux-RT.pdf
Thanks.
Regards,
Aik Eu