Do you only have the default dictionary showing on the left? I wonder if you are adding to a different dictionary and switching back and forth.
You might want to try your previous suggestion - re-install. So make a copy of your clip_entries.ini and search_entries.ini files in the preferences directory and save them somewhere. You can also copy sigil.ini but there is less in there to preserve, or just copy all the files/directories in the sigil/ directory just to be safe.
Remove the files/directories from the preferences directory (everything under sigil - this includes your dictionaries but you've said there is nothing in them...and you've copied them...)
Test adding words to the dictionary again.
You can then stop Sigil, copy back your clip_entries.ini and search_entries.ini to the preferences folder, and restart Sigil.