You don't mention in your post which Freescale chip you're using.
I guess from your "user name" that you're working with an MCF5282.
Get the "Coldfire Init" program from here, it supports the MCF5282:
http://www.microapl.co.uk/Porting/freetools.html
You've probably forgotten to configure the output pins from their default of being GPIO to being dedicated timer pins. Look in the GPIO chapter. The Coldfire Init program should help you with this.
Tom