We are having the same issue here with our view maps in a TW2 project. Like Keith already said - it will still publish in the correct settings but when we open them in AC, it ignores the layer combination setting. It is affecting a large number of section views so it does not make sense to recreate them.
On another project, double-clicking the view map did not take me to the saved zoom area. It updated all the settings, but not the zoom. And even after another save as current zoom, it would not update. In that case, I ended up redoing those specific view maps. These views were not part of a cloned folder.
We also have the latest hotfix installed so I can say it does not seem to correct this issue. Reloading the file from server did not correct it either.
I have attached an image showing the section in view map, the designated settings, and the actual settings after double-clicking on it. Please note the exclamation icon next to the layer combination. When hovering my cursor above it, it said "The settings in the frontmost window no longer correspond to the original view settings." No view settings were modified after double-clicking on it. Hopefully this could be discovered and corrected by those who need to know about it. Thank you.