Garrick
I think this is the issue that you are seeing
1) I have a Plan View Open and I have the View Filter "My Filter" applied to that view.
2) I open the Alignment Editor - if you look at the Tab for the Alignment Editor you will see that it is "Black Text" and the Plan View is "Grey Text" so the Alignment Editor is the Currently Active View
3) I change the View Filter from My Filter to e.g. a View Filter called HAL only - however the Plan View doesn't change - this is because it is not the currently Active View - to change the Plan View - you need to click on the Plan View Tab to make it "Black Text" i.e. the Current Active View and then you can change the View Filter. It will show you the View Filter that is applied and you should still see it as My Filter until you make it the Active View and then change it to HAL only and now the Graphics and Tab will update.
While the Alignment Editor is not a Graphical View and therefore View Filters do not apply, it is still treated as a View and when you change the View Filter while it is active, it is still treated as though that change was applied to the Alignment Editor View because it was the active view. We have to be consistent here whether we have 1 or 10 graphics views open and we likely would not want all 10 graphics views to update with this type of change.
Hope that this helps
Alan