I found solution myself. I don't know whether you suggested it, but it wasn't clear for me from this thread.
Anyway, go to xcode -> preferences..-> accounts. You have to add another account. What is confusing is that here I used to store only appleID which I used to login to Apple developer portal (for getting all provisioning profiles and signing identities). Now, if you are a member of more than one publisher on itunesconnect, you have to add that profile. Basically, you have to put your Apple developer id sand itunesconnect ids, all in the same basket. itunesconnect id doesn't have any provisioning profiles in my case because I use alias just so I can publish apps for many publishers. But it has to be there.
Apple developer account and itunesconnect accounts are not connected, I think apple developer account is there for you to get your certificates and to sign your app, and itunesconnect account is there to upload your apps. It would be nice if it wasn't that confusing. Or not (I'm that much confused!).