Karl:
By default, support for the CF interface on the Altera Dev Boards is enabled in the kernel. Your compile failed because it could not find the appropriate definitiions (na_ide_ide) for this interface.
Did you use the .ptf file we supplied with the distribution or have you created your own Quartus Project? If you did use the .ptf file we supplied (found under nios2/examples/verilog/<board>/linux/), can you check whether the na_ide_ide symbol was created in nios2_system.h (found in your workspace for the kernel, probably nios2/bin/eclipse/workspace/<whatever_you_called_it>/build/include)
If you created your own Quartus Project and you wish to use the CF interface, you'll need the Compact Flash Component. If you don't care or don't want to wait for the CF Component, you can simply disable IDE support (in the kernel configuration, under Device Drivers->ATA/ATAPI/MFM/RLL support) and the compile should complete without further ado.
mike