BlackDex is correct, the Reference mode can find more but doesn't always do so. In other words: the Normal and Reference mode usually always give the exactly same results (i.e what errors they find), but the Normal mode is usually a bit faster.
All previous versions of the product have been using the Reference mode, the Normal mode is a new feature of the new registry cleaner engine included in the PT 2006.
I have now fixed the bug reported (the Normal mode is always selected by default, the previous setting is not remembered), and information texts are now made more clear.