[KevinH]

Yes it definitely sounds like something is very broken in either saving to the settings file or reading from the settings file. My guess is some anti-virus or other program is interfering with that.

As for using multiple Sigil programs at the same time, please do understand that a single settings file is shared by all instances of Sigil and are updated/saved upon Sigil exiting.
So if you change a setting in one Sigil program that is running and exit that version, then later exiting a different running version of Sigil without those changes, when its settings are saved on exit, you will lose you earlier changes made in the first version as those of the last version saved will overwrite any earlier changes.

The last exiting Sigil running programs settings will be what gets saved last.

No idea why you are having trouble with clip but again they need to be loaded from a ini file so perhpas the problem is the same mechanism is at work.

As for Sigil's epub3 Metadata Editor, it will not allow nor keep non-spec metadata. So a non-spec "calibre::rating" stored inside a meta with an unknown property is not supported on purpose. I can look into relaxing that constraint but I would need a list of "alternative" metadata that many people want to add, and I can add support in Sigil's epub3 Metadata editor for them.

But Sigil 2.8.1 should no longer mess up custom legal epub3 metadata as that was fixed. If you can get Sigil 2.8.1 to do that, please let us know exactly what you are doing and what you are trying to add to the metadata, so we can recreate it exactly so we can track it down and fix it.