As a followup to this issue:
The startup drive on the server has failed (i.e. SMART status failure), and it seems this issue (above) was an early sign of the hard drive's failure.
I have a new startup drive running Mac OS Server 10.8.3; installed FMS12A; everything seems to be behaving as expected now.
I would like to close this Bug Report.
No, this bug is not related to the SMART Status of a hard drive or a failing hard drive. This bug happened to us on TWO MACHINES with perfectly fine hard drives... we even bought a ***BRAND NEW MACHINE*** to try to solve this problem. Each machine's hard drive is TOTALLY fine. The SMART status has been verified... Disk Utility reports no errors... hardware test reports no errors... Disk Warrior reports no errors... and the schedules keep disappearing. The full thread of my report is here: