FYI: We have CodeWarrior 6.2 (Rev B) installed.
MCF5329EVB.cfg and MCF5329EVB_FLASH.cfg are used for Boot Flash (2M size Intel). Code Warrior doesn’t have a cfg file to support NAND flash (16M). You must add NAND configuration (CS2) in MCF5329EVB.cfg. What NAND flash do you have? If CodeWarrior FlashProgrammer doesn't have support for this flash type you can add it using a Perl script.