You need to use a 3.x version of the FRC libraries with the 3.x compiler.
You might want to look at Kevin Watson's remake of a default program. It has 2.x and 3.x libraries for both the 8520 (2004-2005) as well as the 8722 (2006-2008) versions of the FRC Robot Controller and is better documented:
http://kevin.org/frc/ifi_frc_simple.zip
MPLAB has some options you may have missed that need to be set correctly.
Double check the settings under
Project->Build Options->Project
Specifically,
- the ones for Include Path and Library Path under the General tab.
- The settings under the MPLAB C18 tab/general. I have -D_FRC_BOARD and use the Large Code/data memory model
I won't have a machine to test and troubleshoot the latest compiler on until after New Years.