Hi Scott,
There is two places that you should check your settings.
1. On the menu bar: - Tools/Equipment profile manager, (create a profile of equipment and give it a name) These settings are for all new sequences I think.
2. The other is the control panel, Icon that looks like a camera along the top bar where the icons are. These settings are similar to the ones in the equipment manager, however they are for the sequence that is open. These settings over ride the equipment manager settings, so I am thinking you have them set in the equipment manager but not the control panel.
Hope that helps. Let me know if I got it wrong or am on the wrong track.