Now I can explain why could CutAndPaste feature got broken. This is a bug which caused hundreds of emails and endless hours of frustration.
Up until version 1.5.27 the behaviour was following:
Right-click context menu sets TotalFinder’s “context of operation” for subsequent cut attempt (context may be sidebar, file item, toolbar, etc.). This context is tested during cut operation and validation of menu items. I had a special condition there which disabled cut for “container” contexts which seemed like a reasonable behaviour. The problem was that this context stayed set until next opening of right-click context menu elsewhere. In other words context of last context menu determined future cut menu item availability (including keyboard shortcuts).
The problem why it was so hard for me to reproduce was that I never tried to click specifically into empty background window. I always tested it right-clicking some files. And didn’t see any clues up until now from @danderson.
I’m so glad. @danderson you deserve a bounty. Please drop me an email to antonin@binaryage.com with your bitcoin address, I will send some funny-internet-money your way 