Not sure about the 2003/2004 confuser, but when I did my PPL in 2003 some of the answers correct when Thom was wrong and some were wrong when Thom was right.
Two that spring to mind are:
* The method for calculating cloud bases was correct in the Confuser.
* The correct given answer for the effect of flaps on pitch was wrong the Confuser.
There were others that I can't recall, suffice to say that they were pretty obvious contradictions so shouldn't cause any grief.