Note that now the Pololu AVR library has an OrangutanPulseIn library that makes it simple to read RC channels (it handles all of the pin-change interrupt code for you). This portion of the library isn’t yet documented in the user’s guide or command reference, but I wrote a forum thread about it that might help you learn how to use it:
I will be documenting it soon. If you’re having trouble with the 3pi RC code, I recommend you try the OrangutanPulseIn library functions.