I can't reproduce that, iUndelete can restore multiple folders. Are you selecting multiple folders?
Note that the *right* pane is where you select files and folders you want to copy. So if you want to restore all subfolders of 'folder001', in the left pane you select 'folder001', then in the right pane select the first sub folder, and while holding the SHIFT key select the last folder you want to restore. Both selected folders and all in between are now selected. Then click 'Recover selected'.
It is currently 4:23PM EST on February 16, 2010
Yes, but we are not in the US but in Europe, so here it was almost bed time, 10:23:39 pm, while you were posting.