OK @darwin , I think I figured out the problem and it’s my fault. For a few years now, I’ve been using a custom icon for the Visor pin button (sorry, not a fan of the slightly purplish default button) by overwriting the two necessary icons in TotalFinder.bundle with these:
It’s usually the first thing I do after installing a new TF version, and this time was no different. Now, however, it would appear that modifying TotalFinder.bundle is a no-go.
Re-installing TF 1.9.0 with SIP disabled (without altering TotalFinder.bundle) and then re-enabling SIP worked fine and everything is working properly. Just with a purple icon. 
I don’t suppose you have any interest in using my icons? They really do match the system color scheme better! I’d be happy to send them to you. 