I’m running KDE 4.1 on openSUSE 11.0. openSUSE Updater (KDE4) keeps bugging me to install the patch “desktop-data-openSUSE-extra-gnome”. I checked and that package isn’t even installed. When I tell the Updater to go ahead and install the patch it goes through the usual process of asking for the root password, then it gets to “Updating…”. It then stops and starts from the beginning to where it tells me the same package needs updating. I feel like I’m stuck in a temporal loop and every time I get to the end of the tunnel I come out on the other side. Argg!
Maybe it sound silly, but how if you turn off the updater applet (don’t allow it to autostart) and do the update using Yast -> Software -> Online Update?
I have noticed this as well, somtimes I need 168 updates and when ok click install, I get 168 errors. The same advise from me: stop the auto-update, like Beagle, it is not worth running it.
Update at your own convenience 
Use YaST !
Usually I just click K-Menu->Computer->Install Software and tell it to update all.
Beagle has been replaced in KDE 4.x with Nepomuk/Strigi.
I’ve been playing with the KDE 4.1 Live CD for the past few nights. I’ve never seen this problem. BUT the very first thing I do with the live CD is enable the repositories for OSS, NON-OSS, Update, and Packman (and no others). Did you try that? I then get a couple dozen packages installed, with no hiccups.