replacing crystal with TCXO

Krupski:
Actually, I'm not sure the test is working properly. We should be seeing either 00:00 or 1:59 if the glitch is present (correct)?

No, the result will either be 1:00 (correct) or 1:59 (glitch). There is no way it will ever read 0:00 (edit: unless you reverse the order of the reads).

Krupski:
Question is... it it "legal" to re-enter the function from inside itself? Will that leak memory, or does C handle stuff like that?

It will. It's called recursion. It's fine as long as you have enough memory for the stack to expand and then contract again (edit: and your function is reentrant). Generally it's a bad idea on a microprocessor with limited memory. And there's no way you can justify it in this case.

I really am amazed at the contortions you're going through to avoid the obvious solution.