I too am having a hard time. I have a MBPro and a MBAir. The Air is the latest purchase. Both are registered with Apple. My problem is that I can no longer update several programs on the MBP, which was the computer where I originally purchased the items from the App Store. It shows them listed in the "update" location or in the purchases location showing the "update" button. When I try to update them it comes back and tells me that it is not the original account. This is very recent and for the life of me I cannot figure out where the problem has come from. I checked the ID via the store and they are exactly the same.
Very frustrating. I don't like the app store because there is no way apps I already own can be brought under the umbrella for updates and there is no way to demo an app! The store is a good idea but they need to find resolution to those two problems. Some developers no longer offer demos at their site because all runs through the store. Don't object to monopolies if they are at least benevolent ;-)
Help really needed with this ID thing - it impacts both free programs and purchased ones. For example, one of the programs is Byword. I wrote the developer and was told I can have up to 5 Macs using the same program (great support staff there, by the way! Top notch and prompt), so there is no problem with the license on that one and it is through the store I got it on both of my computers. It is blocked. Same with Kindle app.
Thanks for any help you can give me.