The Default Layers (Master) dialog and the Bid Layers dialog, accessed from the Image Tab, are two separate lists. The Layers dialog box, opened from within a Bid, is unique to the current Bid while the Default Layers dialog lists the Layers that are automatically added to new Bids.
Don't mistake the "Default Layers" list with the Default Layer that is added to every Bid (always highlighted in blue in the Layers window). The Default Layer is where the program stores all takeoff created with Conditions not assigned to a specific Layer is stored (the "Default" layer is a Default Layer - a good nickname for the "Default" layer is "unassigned").