I can’t remember exactly, but I think I had to Save As a new customization to change it. I don’t think you can change these things once it is saved like the All Companies checkbox.
We had the same issue, the customization list was not showing the actual customization I had created for that particular module. I went to customization maintenance, and found out the customization name was already been used for another module. Re-saved the customization with new name and it worked.