I installed all of these via CKAN.
Walkthrough of reproduction
Fresh install of KSP 1.4.3. Through CKAN installed ToolbarController, ClickthroughBlocker, Antennae Helper, Part Wizard. In VAB, you can see buttons for Antennae Helper and Part Wizard. For some reason this time I didn't get AH in the TB options, but Part Wizard and ToolbarController twice, but no Antennae Helper. First time I've seen that happen.
VAB with Toolbar Controller, Antennae Helper, and Part Wizard buttons showing
KSP.log
output_log.txt
Exit game. Through CKAN, uninstalled Antennae Helper and Part Wizard, and installed KSPCasher and Hangar Extended. Toolbar Controller still only has options from after the first install.
KSC with Toolbar Controller and KSPCasher buttons showing
VAB with Toolbar Controller and Hangar Extended buttons showing
KSP.log
output_log.txt
So, it IS putting the right buttons where they should be, just not updating the Toolbar Controller Options window with new buttons.
EDIT: CKAN left the folders for Part Wizard and Antennae Helper after uninstalling them, and show up in the "Folders and files in GameData" section of the second KSP.log. Manually removed them and re-ran KSP, same result.
VAB with Toolbar Controller and Hangar Extended buttons showing
KSP.log
output_log.text