This is reproducible every time using the “Open file… window” of any application (or for that matter Adobe apps) and happens on the generell finder window randomly.
Im using TF 1.9.0 on macOS Sierra 10.12.3
Standard system open/save dialogs are not implemented in Finder.app. They are implemented by system libraries. It is a different code which only mimic Finder’s look & feel. I’m sorry I cannot really change its behaviour with TotalFinder.
That is a shame as I’d really like to see this be consistent.
Thank you for the explanation though.