I've run into a lot of problems with up2date in the past. I find the yum updater that comes packaged with Fedora Core to be much better and easier to use.
To update with yum, open a terminal, then type:
If you need any more help, just write back.
If you really really want to use up2date, sometime I find problems like the one you described are worked out by running up2date over and over until it works.