Gawd, I was steaming over this for a month...thanks for answering to this post!
I love my 'droid but I sure wish it had come with more than the minimal "user guide". They tell you that you CAN do something, but they don't tell you HOW! I almost looked for a "Droid for Dummies" book...but I'm glad I found this forum first. Wish I knew how all of you got so smart without a manual!
I have a similar problem, I sync my Droid Incredible with ACT! Pro 2012 and when I call from my mobile, on some of my contacts the number rings their fax. Sure enough in the Android contact list, their fax is set up as primary! Not most of my contacts but I have called 3 - 4 fax numbers in the last month, annoying, specially on the road. I will contact CompanionLink and ask why.
This post is rather old, and this method does not work for me with a Samsung Galaxy 4, Android 4.3. I don't know if it's a difference in Android version, or whether Samsung has replaced the Contacts app with their own. In any case, the following works for me:
Go into contact in either the Contacts or Phone app (there is no People app any more). Select the menu, and click "Mark as default". That will give you a list of phone numbers (and email addresses) and you can select the one you want to be primary/default.