The configuration box for each bar is correctly remembering the intended state, but, regardless of whether the click-through box is checked or not, the functionality is always turned off after a reload/relog.

To reproduce it I turned off all other addons and turned click-through off then restarted my game. After logging in click-through is off as expected. I turn it on by typing /dom and clicking the configure bars button, then right-clicking Action Bar 1 and turning on click-through, then closing the Action Bar 1 settings box, then clicking exit on Configuration Mode box. Click-through then works as expected, until i do a /reload or log off then back on, in which case the bar can be clicked again despite the Action Bar 1 settings box saying click-through is turned on.

Dominos version 9.0.3-Retail
Retail WoW 9.0.1 (36230)

Forgot to mention that yesterday I tried deleting my dominos WTF files and reinstalling dominos but the same thing was still happening.
Deleted retail\WTF\Account###########\SavedVariables\Dominos.lua & Dominos.lua.bak
Dominos version 9.0.1 or 9.0.2 i don't remember.