OK after you installed handcent did you go into your default message application and turn off notifications, generally when you get the same message twice its from multiple apps doing the same thing, hope this helps!
I am having the same problem on my OG1. I have been using handcent for a while now. This problem just recently started on my phone. I checked all of my settings and everything seems fine. I am wondering if this is a Verizon issue or Handcent? Maybe I'll stop using Handcent & see if the problem resolves.