Those problems sounds very interesting and some of which I have never encountered on these forums, some ive never heard of so far.
Thankfully our upgrade went well.
We are running FC4 ( old I know, but stable )
I also use yum, including the SecureTeam updates for it, which use enhanced secure platforms,....or so im told.
Generally, all our systems work perfectly off the bat, we have tested every function in the control panel and clicked every link, they work fine so far.
I'll run some tests on the server matching the problems you mentioned, see what I could find.
What kernel are you running btw?
2.6.17 #1 SMP Tue Oct 24 00:27:54 GMT 2006 i686 athlon i386 GNU/Linux
Thats one of our current systems running up-2-date software.
Have you found anything like the problems you mention in these forums?
I will keep you updated on my findings tomorrow
PS: Have you tried disabling Watchdog, first from its own menus, stop monitoring, then disabling it completely? We had a problem once with that on a previous version, much like what you describe.