I doubt any spectrum analyzer will be off by more than a few tens of ppm, so I expect that 43.52MHz is accurate.
Interesting number. Exactly 17 times 2.56MHz, which is useful since it's 2^8 x 10kHz. I doubt that's a coincidence.
I don't know what else you have on your board, and what it else it does when the ethernet link is up, but I feel like there's a clue there.