Do you have some examples? I have developer mode enabled and have never seen any apps complaining (and I have used a lot of different banking apps).
1. Ensure Droidify is not running. 2. Launch it. 3. Tell it to install or update to an app. 4. Receive an Android system prompt to approve the install/update. 5. Approve it. 6. Tell Droidify to install or update another app. 7. Reveive a system prompt to approve the action of step #3 again. 8. Approve it. 9. Receive system prompt to approve step #6. 10. Repeat #6 through #9 for more apps.
Workaround: Do steps #1 through #5.
Foxy Droid doesn't have this problem, but won't auto-download updates for you.