It took a bit of digging to find the fix for this. I regularly upload applications for different companies to iTunesConnect. Imagine my surprise when I could upload an app to my own account. I found lots of threads helping Windows users but none for Macs.

The solution, on Mac OS X, can be done one of two ways. You can delete the .plist files in ~/Library/Preferences/
com.apple.itunes.connect.ApplicationLoader.LSSharedFileList.plist and/or com.apple.itunes.connect.ApplicationLoader.plist
I’m not sure which one applies but it forces Application Loader to run the “Set Up Wizard…” again (“Set Up Wizard…” can also be run from the Window menu.)

After which you will be prompted to log in with the correct Apple ID again.