I have org version 9.0.3 (and I've been noticing this the whole time I've used org - only just now reporting it), and this is 100% consistent for me.
I often have two client frames open, connected to the same emacs daemon. One frame will be displaying the org agenda (I'll call this Frame 1), while the other (Frame 2) displays one of the backing org files (e.g. ~/org/ todo.org in my case). When both are open, and I attempt to reschedule an entry through the agenda view (so, I have Frame 1 focused, and I enter all my commands there - in this case, with M-x org-agenda-schedule), everything initially appears to be working. I get the minibuffer prompt to enter a new time, which is correctly defaulted to the time of the entry I'm on (in Frame 1). However, once I hit Enter to complete the action, it's applied as though I had Frame 2 focused. Whichever line my cursor is on in the todo.org buffer in Frame 2 is rescheduled, while the entry my cursor is on in Frame 1 is unmodified. If I close Frame 2, everything works perfectly. I assume that there's some logic that figures out where in the actual backing org files to apply modifications that the user makes to entries in the agenda view, and that logic is broken when the backing file is displayed in another (unfocused) emacs frame. I run emacs on a Linux (NixOS) system, using i3 4.13 as a window manager. - Anders Papitto
