From a technical standpoint, they rank the same. Google doesn't give special treatments to .coms. However, you may be losing some links by accident. I had a popular .org site a while ago, and found that a lot of people mistakenly linked to the .com version of my site (which was a parked domain) because they didn't realize it wasn't .com. I imagine you'd have some similar problems there.
Ya, I actually purchased a .net tld and noticed that I was building links for someones parked .com. I just got so used to having a .com myself that I made a huge mistake and threw away several hours of link building.