You can now install the new Clockworkmod recovery 18.104.22.168 on you Transformer Prime. The update has a lot of changes and improvements like the following:
Possibly fixes bricks (by properly restoring boot.img).
Correctly comes with Staging/System unmounted.
Nandroid Restores properly the boot.img (of backups created with this CWM). This means no more issues when restoring a Rom if you are coming from another from (for example, if you are restoring Virtuous after wiping cm9).
Backups are now about 10x faster.
Restores are a bit faster (not as dramatic as backups).
CWM Recovery lets you flash Custom ROMs and other hacks on android so that you can customize your phone more.