I went thru all replies in this thread without avail. Repaired disk permissions and re-built spotlight index, several times, controlling via console if indexing went fine. Always, this annoying and uninformative message "You have updates available for other accounts. Sign in to (null) to update applications for that account." (Why does the appstore not tell which account ?)
Finally, I sorted it out, kind of.
I have two Apple-IDs in the app-store (ID1, ID2). I have two laptops from where I purchased apps (MBP-2008, MBP-2011).
On MBP-2011 I could not update from Xcode-4.6 to Xcode-4.6.1. Xcode shows up with the "update" button, but update failed with "wrong account". This is clearly a bug on the app-store, since Xcode is free. There should be a possibility for a fresh install no matter what. I finally found Xcode-4.6.1.dmg for download on bittorrent and did a fresh install.
I had purchased Yojimbo-3 from ID2 on MBP-2008 from the App-store. My hard disk was propagated from MBP-2008 to MBP-2011 with Yojimbo on it or Yojimbi was migrated using migration assistant; I do not remember. I faced the same problem with update from Yojimbo-3-0-2 to Yojimbo 3.0.4 on MBP-2011. Update refused because wrong account (tried from both accounts ID1- and ID2) . However, I could update using my prior MBP-2008 using ID2. I copied the executable to MBP-2011. Starting Yojimbo-3.0.4 for the first time on MBP-2011 I got a message like "This was purchased on another computer (!!!! now you got it correct Apple !!!), sign in with your Apple.ID." So I signed in with ID2 once and all is fine.
Bottomline:
1. messages from the app-store are completely confusing, even wrong.
2. It should be possible to download FREE apps again (rather than update only), no matter what.
3. Do not purchase from the app-store but from the software vendor directly. In many cases, you have a serial number and support.
4. The update procedure via app-store is fundamentally flawed compared to old Snow Leopard times.