You don't state which flash you are using. I am using Intel 28F128J3D. There is support in CW 6.3 for the J3 part which according to the datasheet has the exact same commands as the J3D part but CW 6.3 is broken when it comes to programming the Intel 28F128J3D. When I asked Freescale support the response I got was that I am not using a Freescale Eval board and they don't have anyway to figure out this problem.
To get arround this problem, I use a program called CFFLASHER.EXE. I don't know where this was obtained (person who got it is no longer here) but it does program this part and many others. It must have been supplied by Freescale but honestly I don't know. Unfortunately it is a major pain because you have to get out of the IDE to release the P&E dongle so this external Windows flashing program can use the P&E dongle. Furthermore, once you are out of the IDE, the P&E dongle seems to hold down the eval board's bus so it won't start from flash if you reset the eval board. To get around the reset hold-down you have to unplug the dongle and power up the eval board untethered. It is a big PIA - debugging in the stone age.