If I have two iTunes accounts, and only want one to update my apps why does the other account keep opening?

Here's the issue-I have two iTunes accounts, yet account #1 always comes up when I want to update my apps. This occurs even when account #2 is logged in and has been synced from desktop to iPad. Additionally,Account #2 is logged in on the iPad and yet account #1 prompt appears when updating. Interestingly account #2 functions normal for iTunes purchases but not apps purchases. Any suggestions?