I had the same problem with my new Mini where I couldn't update the pre-installed iLife via the Mac App Store. I was initially instructed by Apple Support to wipe it and reinstall Lion. After a reinstallation, I no longer had any of the iLife apps. I clicked 'Accept' in the Mac App Store and received a message saying the apps had already been associated with my Apple ID and then they disappeared from my 'Purchases' tab.
I had a number of calls and email exchanges with a Senior Advisor from Apple Support. I did the 'packet trace' thing with them, all while I was in contact with iTunes Support as well. After relaying back and forth beetween the two different support groups, iTunes Support finally told me to buy all of the iLife apps from the Mac App Store and they would reimburse me. I asked Apple Support if this was the best option or if I should wait for the official fix. They told me to take the reimbursement option. When I asked iTunes Support if they could give me redemption codes they said that none existed and they would only reimburse my purchases.
After buying iLife '11 from the Mac App Store, I now have the apps installed on my computer and they are properly linked to my Apple ID. I am still waiting for the purchases to hit my credit card and if they do I will wait to see if I am reimbursed.
My recommendation to everyone experiencing this problem:
Do not wait for the 'fix' to come out if you have wiped Lion or are sick of seeing the update notifications. Contact iTunes Support and have them help you obtain the apps 'officially'.
This is pure speculation, but I'm of the opinion that this will be the resolution in the end, for everyone to just buy/redeem the apps from the Mac App Store. The official fix will not be retroactive but only prevent new Mac's from having this same problem in the future.