It looks like adjtimex() and/or adjtime() is not implemented in a way that ntpd is expecting. One recent example of this is:

http://bugs.ntp.org/871

Because of this, we're about to at least recommend (and at most enforce) that the -x option (slew always) option for ntpd under linux be disabled.

I'd be happy to coordinate and/or work with somebody to address this issue.

Harlan Stenn