I've dowloaded the file and tryed it out with my evolution version.
It's to big to compile it - sorry.
The Port settings are to made in the "Project|Configure|C Compiler|Libraries|Graphic Display menu" folder.
In Your Project is used the PORTA for DATA 0...7,
and PORTC for the control Pins.
Possible bug's can be made with the fuses.
Do You have disabled the ATMEGA 103 compabitility Fuse?
Have You disabled the JTAG Fuse - when not using?
JTAG uses some pins of Port F of the ATMEGA64 and should make no trouble here, but I guess it's better to disable it.
Some Hardware errors with the cabelling of the Display are possible too.
Please refer the Datasheet of Your used Display to check the cabelling of the additional Parts.