Having the same problem, same circumstances. Did you ever get this sorted?
I'm compiling for 3.1.2/2G on Ubuntu 9.10. My research so far indicates that I need the arm/iphone lobjc and what I have is the intel/linux lobjc. I haven't figured out where to get the correct libraries.
Sorry, which folders? path/toolchain/toolchain/sys/usr/include and System/Library/Frameworks? I'm having a heck of a time finding the correct google code page with the search.
sorry, it was the usr/lib folder and frameworks. Scroll down to the comment I posted on dec 17. There's a link to an explanation of the problem as well. Sorry for the crappy replies - I'm posting from my phone so it's hard to type.