I have a key to Pelatus C-12 showing an inactive key on my keychain, but when selected and inspected, lists station access as though it's active.

I do have the key manager plugin installed, which also shows it as an active key, its just not blue-lit on my keychain.

I have had the opposite problem with keys showing as active when they weren'i...
I don't have any plugs that fiddle with the keys

Just because you have no plugins that can alter keys is not enough, have you tried running plugin free?