Gregg,
You might want to download the new hotkeys guide for Eos/Ion. Ctrl 1-6 as well as Alt 1-3 changed in the release of 1.4--There are a few other changes to the hotkeys in v1.4. Remember if you are trying to display the direct selects onto the screens you can always use the browser. Displays-->Browser-->Virtual Controls-->5x10 Direct Select Module. You can do the same for the onscreen faders as well.
As for the other question--Check your User ID number. It could have been reset once you loaded the new version of software. Remember that if you have both devices with the same User ID then they will share command lines and live/blind states. To change this you can go into Setup-->Desk Settings-->Displays within the console itself or go through the shell and change it in Settings.
Hope that helps.
Eos Hot Keys Quick Guide for Software v1.4.0 :
http://www.etcconnect.com/docs/docs_downloads/techdocs/Eos_Hotkeys_v1.4_QG_RevA.pdf
www.etcconnect.com