I am able to reproduce this every time (in fact it's really wreaking my project.)
Steps to reproduce:
1. Create a PCB Library document (or use an existing one.)
2. Create a component.
3. Add a pad
4. Edit the pad with the attached settings
5. Click Ok, this pad should look like the following (this is a pad to act as a bottom footprint on a module.)
6. Save the PCB library, and close it.
7. Re-open the PCB Library.
8. Observe the pad now has the following settings:
and looks like:
Workaround:
Use two separate simple pads for every pad, one multilayer and one bottom layer only. Not very pleasant.
