Hi @gudjkrist,
It's been over a year and I don't see anyone else addressing your issue.
Are you still having this problem or did you find a solution or workaround?
I've been working with Spaces a lot -- I currently am using about 30 of the 45 I have created. I have tried many different approaches to the problem of getting applications to reopen in the space that I want them to. In most cases for me, this is after a reboot. In another case, to switch Spaces I activate an app that has a little window on each Space. Unfortunately, when I switch the Desktop focus to a new space, that is the frontmost app. And being unobtrusive, I don't notice and I often begin to type or paste in what I imagine is the frontmost app, so my typing or pasting gets captured by the little Desktop Space ID window. I'm working on ideas to fix that.
So I have some perspective on what might be going on that is annoying you, Gud, if you're still interested.
In brief, when Zabobon's system attempts to open an app that is part of a workspace, if it's already open, then the MacOS decides that it's not necessary to either open it again or move it. It will just take your focus to the Desktop that already has the app. That's the OS.
Zabobon would have to look for the app being already open and then use a different operation to open a new window in the app, if the app even supports that, or move the existing window to the desired Desktop. I move windows between Desktops a lot and a use a system similar to @_jims's "MACROS: Desktop Spaces • Macros to Improve Navigation and Window Management, v4.0".
I'm pretty sure you would need to write your own window-moving macros that mimic the basic window moving process: click and hold the mouse on the window title bar, then switch Desktops, then release the mouse. You would have to insert that with the necessary testing logic into Zabobon's system. Or write it as a cleanup process if you detect an error in the constructed Workspace.
That's for already open apps. For poorly behaved apps, it's a different story. Some apps are very good about spaces, some adequate, some annoying, and some seem downright malicious. For instance, whenever I reboot, I can count on my KBM editor always being right were I originally put it, in Desktop 13, which I call "[K] Keyboard Maestro ⌥⌘K". (I put both the menu choice and the hotkey for the Desktop into the name, it makes many things so much easier to do. I change Spaces by menu or hotkey, so if I add or remove Desktops to the left of "[K] Keyboard Maestro ⌥⌘K", the number 13 can change without my caring.)
In contrast Preview is very annoying. I can have a dozen Preview windows in Research, Books I'm Reading, Financial Admin, Editing, etc., and on reboot they all end up in whatever Desktop was activated by whichever was the most recent app to restart. And since on reboot apps do not necessarily open in the exact same order every time, all those dozen Preview windows are not consistently in the same wrong Desktop.
Any or all of these issues, and more, could be affecting how you get Omnifocus to behave well with Spaces.
If you could tell me a little more about your current symptoms, if any, I might have some ideas.