Ok, I finally found out the root of the problem or at least how to fix it manually the hard way (if you have jailbroken device, sorry:)).
Information on the accounts used to purchase each application is stored in file
\private\var\mobile\Library\Caches\com.apple.mobile.installation.plist
For some unknown reason (Apple, please check you source code!) all applications on my iPad except the very last one I use to test whether installing already purchased application will fix the problem where stored with one single account ID in this file. I suspect that at some point all ID’s will be rewritten at once with another account ID and vice versa in such a way you will have all applications bought from single account. Account ID in this file is not your e-mail used as Apple ID, it is 9 digit integer number you can find in any iTunesMetadata.plist of corresponding application under DSPersonID
key, or in file \private\var\root\Library\Lockdown\data_ark.plist all account with person ID are listed as well, I think you will be able to find that information a lot of ways.
Unfortunately deleting file com.apple.mobile.installation.plist in Cache folder will not force regenerating it. In my case it lead to unbootable device until I restored file via i-FunBox. I used a copy of the file on PC and proper text editor to replace person id for selected applications I was sure belonging to wrong account. iFile with copy/paste may work as well but I didn’t test it . Very frustrating procedure taking in account I am pretty sure that information will be corrupted by apple very soon. Finally I managed to update my application though I had to reboot device after account change in AppStore (maybe ReSpring will work as well).