Hi Excuse me if this questions in the wrong forum section but now I have bashed my head against this weird issue for some time.
I've modified version 22 of Arduino and made a stk500-compatible bootloader work but have now run into some problems. Everything I've tried has worked like a charm. Now I'm having issues with using PC2-4 as inputs. Since I have multiple robots I can rule out faulty hardware and since the physical design has worked many times before with BASCOM I suspect that it's a software issue. I have checked the Arduino files (mainly pins_penguino.cxx) and can't find a reasonable explanation and now time's running out. One hypothesis is that it's a conflict with analog I/O but I can't find any code that might explain it.
My modified software package can be downloaded here.