I am having the same problem, on my Bold 9000 running 184.108.40.206. My clock will run about 5 minutes slow per day. I have tried "network," ,"blackberry" and "off" source options to no avail. Even if I "update device date and time" during desktop manager syncs, it doesn't help much unless I sync more than once per day.
On a separate note, but perhaps related to the OS build, I leak about 7mb of memory per day. That is, whenever I pull the battery and reboot, I gain about 7mb of application memory.