My wife and I have both had this problem since we've had our phones. She has a Pantech Crossover (Froyo-based), and I have a Thunderbolt (and the problem happened when I was on Froyo just as readily as now that I'm on OTA stock Gingerbread).
We both ended up deleting the "alternate" email addresses entirely from our phones, which is a pain in the tuckus because we both used to check 2-3 Gmail accounts from our phones (and in one case, it was our shared Gmail account), but we got more sick of the missing updates, and apps she installed on her phone showing up on mine and vice versa.
It seemed (with what little research I did) that the Market was sensitive to which Google account I had logged into the most recently to determine which account to install the app under. So I ended up with a sordid mess of some apps under one account, some under another, some under an account I had deleted so they were never visible, etc.
I ended up deleting all the "extra" accounts and went down to one, uninstalled any apps that did not appear in my "My Apps" view, and reinstalling them under the single account.
I still have odd issues with the Market (My Apps will show updates that I've already applied, or be missing updates I know are there), but those seem to be refresh issues, and not misfiling to a different account.