updated, give it a spin, see if that fixes it.

1. On Remote Controller Door, when I click "macros" and cogwheel, for some reason there are two entries of "proximity open".

2. When I select "proximity open" and then click the action buttons, new actions are not added to the list.

3. If I create a new tab (profile?), the + next to Default I, and click the new tab, then click "proximity open", then the cog wheel and all buttons of that toolbar disappear.

so presets replace all current actions and profiles, and can be multi-profile themselves, anything existing actions or profiles get wiped. this also explains most of your errors, being an index error (I can fix that, leave it to me, I'll add in an additional check) your on profile two which no longer exists, index error occurs result prevents the rest of the gui from showing.

use the copy and paste if you want to copy a preset or action list into another profile or door, copy and paste doesn't wipe any existing actions and copies the selected profile only (and paste pastes into the selected profile only).

multiple entries is a weird one, check to see there aren't multiple versions of powerlogic installed (e.g. don't run both the steam version and manual version together at the same time)

I have tried now to deactivate all mods except power logic. I still see two entries of "proximity open". I have only ever installed the mod from steam.