Upgrading with mergemaster works, not freebsd-update?

A while back I had an issue with freebsd-update(8) where whenever I tried to upgrade from 8.2p9 to 8.2p10 it would say nothing needed to be done and that mergemaster.mtree had been modified locally. It then refused to do anything. I also tried upgrading to 8.3. freebsd-update(8) had me manually deal with about 200 files that it thinks changed (just the version line up top) and then errors saying INDEX.NEW file not found about 200 times.

I went with folks advice to use the mergemaster(8) route:
cvsup the version I want (8.3 in this case)
Code:
mergemaster -p
cd /usr/src
make buildworld
make buildkernel
make installkernel
reboot
make installworld
mergemaster -iU
reboot
All seemed to work great. Got to 8.3p4 like I wanted. I decided to check freebsd-update again just to see what happened. It said some files needed to be upgraded for 8.3p4, so I let it. It downgraded me to 8.3p3 and now says no changes needed for p4 but mergemaster.mtree has been modified locally.

Any ideas what's up with freebsd-update?
 
The update from p3 to p4 didn't change the kernel, the updates were for other parts of the OS. Hence the version the kernel reports is still p3.

By rebuilding from source the kernel used the new version and thus you get a p4.
 
Ok, well at least that part makes sense. freebsd-update's apparent inability to upgrade the /etc files is odd to me still, but at least mergemaster worked.
 
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