In stages...
0 - What CPU are you using? It helps to provide details. What OS is it running? Compiling with CodeWarrior or something else?
1 - If you read the GPIO pin, can you see the signal (that you are using to cause the Capture) changing?
2 - Is the Timer performing the Capture? Is it setting the flag to say this has happened?
3 - Is the request showing up in the Interrupt Controller? Run your test with CPU interrupts disabled to see if the request is making it this far.
4 - Are you programming a Vector in the Interrupt Table?
Tom