I would take a look at http://forums.freescale.com/freescale/board?board.id=CWCFCOMM
since there are quite a lot of problem reports of this nature.
My experience is that CW7.1 (assuming you are using it) has more problems with programming than CW6.x. Sometimes it stops working on my Vista PC and then I have to unplug the cable and restart CW to get it working again.
Don't forget that you can also use CFFlasher (from Freescale) to delete and program. This may work better in some cases.