I had the same multiple contact issue also... and how I corrected it..
First... I told Handcent that I just wanted it to show contacts with mobile numbers... Nothing else.
In PEOPLE, I only show contacts on the phone.... I do not link contacts with GOOGLE... I do link contacts to FACEBOOK. But again, I only tell my contact list to show contacts on the phone.... No Google / Facebook / or SIM.
Now, when I tell it to also display SIM, i have about 100 contacts show up. How they got on the SIM card is beyond me... but there they were.... I deleted ALL the contacts on the SIM....
Once I did this, all my message programs started showing the proper MOBILE number... and ONLY the mobile number... FINALLY!
So, for those having issues, I would see if you have accidentally stored some of your contacts on the SIM card...
Lego