First of all, did these changes your code work with the 2008 KOP GTS?
Also, DivSys, the creators of the boards have said that this problem has existed for 2 years and have offered to fix the boards from this year:
Chief Delphi Thread by DivSys
Finally, you cannot use the 2007 KOP GTS on this year's robot:
FIRST Q & A Response
If you want, you can list the changes that you made or post snippets of code showing how you used KWatson's encoder code, so that we can figure anything out.