This thread has already described much of the mystery surrounding the problem of the ntpd daemon on mavericks. A quick recap:
1. The Mavericks version of ntpd does not adjust the system clock directly, nor does it obey the polling interval directives.
2. ntpd is configured by /usr/libexec/ntpd-wrapper to create and update the file /var/db/ntp.drift. (/usr/libexec/ntpd-wrapper is itself invoked by launchd, via the /System/Library/LaunchDaemons/org.ntp.ntpd.plist file.)
3. The pacemaker daemon is designed to read /var/db/ntp.drift and invoke adjtime(2) to adjust the system clock.
4. To save energy, pacemaker will only run if /var/db/ntp.drift has been updated within one minute of the current time.
5. Though I have not completely verified the effect, I believe that because ntp.drift is a very small file, it tends to remain in the file system cache for long periods of time (even when opened and closed for each write). The file modify date is only changed when the cached data is flushed to disk, but the cache consistency code will ensure that any reads of the file return the proper, updated contents. The unfortunate side-effect is that pacemaker won't be triggered when necessary.
6. This problem may be fixed in Yosemite, thought I don't have one of those system running currently and so have not verified that.
7. As others have noted, if you are not concerned about energy use, you can either compile ntpd from the standard ntp release and use that, or just copy ntpd from a 10.8 system (caveat: I haven't tried that yet).
8. You can avoid simultaneous operation of pacemaker and ntpd by altering /usr/libexec/ntpd-wrapper to have ntpd write its drift file to any location other than /var/db/ntp.drift.