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.
Uninstall Sigil.
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...)
Reboot
Re-install Sigil
Start Sigil.
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.