We have custom hardware running 3.2 Angstrom on a SAM9G45 processor. Everything works fine. Recently we designed similar hardware that uses the SAM9G25 processor. We found the 2.6 kernel works fine on the SAM9G25, but we needed to port the 3.2 kernel to the platform to take advatage of some wireless drivers. We completed the port, but we have just discovered the time of day clock is not reliable. It runs fine for about 20 minutes - then the time (reported by "date") will jump ahead a few hours or days. The 2.6 kernel still works fine, so we think it's something we did not port correctly. We have looked over everything, but no luck so far. I'm not sure where to look next.
Final Answer: Atmel supplies a patch for the 2.6 kernel, to the file tcb_clksrc.c. We missed that in our port to the 3.2 kernel. Thanks for the insight!