Unexpected realtime delay and genserkins

Are you sure you have a H110? That's a relatively current chipset for LGA 1151 CPUs
I would expect something like a P35 G41 or 9X5 series on a Core Duo (a 10 year old chipset)

Your worst case latency is 4X you servo period so its not surprising you are getting real time errors
are these numbers with your 3.5 ms (3500000 ns )servo thread?

If so that's even more mysterious, since that means your CPU clock is about 1 GHz (and there are no desktop Core Duo CPUs
that run at 1 GHz AFAIK)

Do you have the Motherboard and CPU part numbers?

INTEL Pentium Dual-Core G4560
MSI H110M PRO-VD PLUS

OK that makes more sense (that's not a Core Duo that's a current Pentium dual core CPU)

What was the servo thread setting that generated your timing numbers?

Also what does

uname -a

print?

"uname -a" does:

Linux debian22 3.2.0-5-rt-686-pae #1 SMP PREEMPT RT Debian 3.2.96-3 i686 GNU/Linux

ini:
SERVO PERIOD 1000000

OK so that means something is causing ~ 4 milliseconds latency on your system

Do you have all speed-step / turbo modes / power saving options disabled in your BIOS?

Yes! These options are disabled