Just updated my TortoiseSVN client at home from 1.6.9 to 1.6.11 and found that I can no longer use overlay icons, either in Explorer or in Total Commander (more used to the latter).
It appeared as if Tortoise shell extension was not loaded. I tried a restart - same thing. Googled on it and found their FAQ, which didn’t help either.
A little more googling brought me to this page.
Simon, one of their developers, noted this was a common issue and suggested to do a repair. Tried that, prompted to restart, and everything is working fine since then.
I remember trying an upgrade to 1.6.10 with same issues, but I did a rollback at that time.
They might have introduced some breaking changes since that version. Luckily, not so critical.