You may be using the ATMega8 - which doesn't have any PCINT pins at all. That could explain the issue.
Yes Project Designer ( not 'builder'
) does generate other C files in the 'lib' sub folder of your project so you need to use the generated makefile or AVRStudio to build the project. I assume you are doing this anyway otherwise you would have got other errors. And your error is in 'lib/opt_pcint.h' anyway.
What devices are you using? Or better still send me your project file '*.prj'. I am assumng you've tried to use something that requires PCINT pins.
Commenting out code that causes an error may allow the program to compile - but doesn't necessarily mean that the code will work !!