I recommend that you manually install the new Superuser app. Use the following steps to install it manually.
1. Download the "su-2.2.2-ef-signed.zip" file from here
and extract the "Superuser.apk" and "su" files from it.
2. Copy those two files to your sd card and after that remember to eject/unmount it from your pc and change back to "charge only" mode or disconnect the USB cable so that your sd card is accessible from your phone.
3. Install Terminal Emulator from Market if you haven't already.
4. Open Terminal Emulator and use "su" command to become root.
5. Remount your phone's system partition as writable using the following command.
mount -o remount,rw -t yaffs2 /dev/block/mtdblock6 /system
It may not be "mtdblock6" for some milestones, use the "mount" command to confirm.
6. Copy and replace the old Superuser.apk with the new one from your sd card.
cp -f /sdcard/Superuser.apk /system/app/
7. Copy the new "su" file from your sd card to /system/xbin and change permissions to 04755.
cp /sdcard/su /system/xbin/
chmod 04755 /system/xbin/su
8. Remove the old "su" file located at /system/bin and create a symlink to the new one in /system/xbin.
rm -f /system/bin/su
ln -s ../xbin/su /system/bin/su
9. Reboot phone.
After rebooting you should see the new Superuser app in your app drawer. Also, the old Superuser app gets listed as "com.koushikdutta.superuser" in Settings > Applications > Manage Applications. You can go ahead and uninstall that.