Sorry, I should have explained more clearly what it means that the method is private. In short, private methods are not officially supported - they may not have documentation, they may not work, or they may even have unexpected side effects - just like in your case.
There is a private method called 'User Interaction:Compare VIs XML' which is able to compare VIs and generate an HTML report. I didn't test it too thoroughly but I think it's worth looking at. I currently do not have LabVIEW 2012 and do not know if it is available in this version. Compare_Private_17.vi Compare_Private_12.vi