Hiya,
I can't really comment as to whether or not it is the same problem without seeing exactly what you are getting but I do have a bit of a (sloppy) work around to the problem:
1. After I successfully build the ap with MQX, I then click on "Run"->"Debug Configurations".
2. I then click on the "<Appname>_<board>_Int_Flash_Debug_PEBDM" on the left side to highlight it.
3. Next, click on the "Debugger" tab
4. Click on the "Download" (under "Debugger") and deselect the "Execute Tasks" (this will avoid the message when you start up the debugger.
5. Next click on the "Connection" (under "Debugger") and select a different "Connection:" (the one I get initially, which is correct, is "P&E ColdFire V234 Multilink\Cyclone Max") and then click on "Apply".
6. Change the "Connection:" to the original (correct) setting and then click on "Apply".
7. You can close the "Debug Configurations" dialog box and you should be able to program and debug without any problems.
For some reason, CW does not properly recognize the debugger link. To get it working, you have to change it to something else, then change it back.
Let me know if this fixes your problem.
myke