First, I was having issues where my phone was not vibrating with Handcent. I downloaded Sound Manager, hit menu, and made sure that the vibration occured "whenever possible" on notifications, and that solved the problem.
Now, when making a customized pattern, you must enter the pattern in this format:
0,200,100,200,100,200
NOT this format:
0, 200, 100, 200, 100, 200
Spaces will not be recognized and will null your entries...