Every time i try to skip the first Bowser cut scene on Pinna one, it takes me to the title screen.

If it is the first cutscene where mecha bowser appears you may be exiting area too early, but I dont understand how it could take you to the title screen.

Yeah it happens if you use the practice codes.

It should be fixed in the latest version, try downloading them again from http://gct.zint.ch/