There has been loads of threads on here mate with stage 3 k04 cars not quite making the same power as edition 30s / s3s / cupras with stage 2 + and a few tuners suggested that to me aswell thats one of the reasons why i chose not to go stage 3 and sell my GTI, maybe your car just produces a bit more, and brings it in line.
then again it could be due to different RRs