>> Could this change have caused an error like this?
>> Nov 3 07:38:09 struck ntpd[402]: time error 2069188655 over 1000 seconds;
>> set clock manually

 I haven't had any problems since then.

> Could you try to boot an old kernel after the new kernel (or vice versa)?  If
> the kernel doesn't print any WARNINGs about clock on mountroot, I don't think
> mk48txx changes (which are only internal API changes) have any problem

 I booted a GENERIC kernel from Oct 30th and then back to yesterday's kernel
with no problems other than the clock losing a second at each boot.

> and I'm afraid ntp would have some bugs (around LP64BE?)

 I think so too.