I’m running DT v3.0.4, on my 2019 16" MacBook Pro (running v10.15.3), with Safari v13.0.5 installed. In Safari, I have the Clip to DEVONthink v3.0.3 extension installed, and as I watch the toolbar, the extension is “blinking” there/not there. It doesn’t matter whether DT3 is launched and running or not.
DEVONthink 3 provides only the extension but its usage and installation is completely handled by Safari. Does a reboot fix this? Or a reinstallation of the DEVONthink 3.app?
Workaround: When showing Safari Preferences -> Extensions: Change to Advanced tab and back to Extensions. The tick boxes work now. This has worked for me.