I won't have time to look into the code you posted until later, but if you haven't already done so I suggest it would be worth your time writing a minimal sketch that demonstrates the problem in the simplest way you can.
I assume that a simple sketch that just calls millis() repeatedly and prints the result won't reproduce the problem, because it didn't for me.
Something else you're doing within the sketch must be triggering it, and the suggestions that it's interrupt overflow seem like the most likely explanation. However, that would not occur on a well-behaved system.
You may find it's something that can be provoked by doing SPI writes, or SPI reads, or something else. If you can figure out by trial and error what the key factor is, that would help us understand the cause and get us closer to finding a resolution.