As others have commented, sometimes changing monitor profiles in DisplayFusion messes up the ID numbers Windows assigns to the monitors. In my 3-monitor case, some elements stayed with the correct monitor while others got swapped between monitors 2 and 3.

If playing around still doesn't get things back right, the fix is to force Windows to rediscover the monitors one-by-one. You have to delete two registry keys, then plug-in the monitors one at a time and restart. Apparently this is a known problem in Windows and has been since Vista. Here are links to read more about it along with step-by-step instructions.

See last post in this 7-year-old thread!:
https://social.technet.microsoft.com/Forums/office/en-US/30b16266-cbc6-4759-8c30-8d10b46fb7c6/changing-monitor-identities

And this one:
http://support.displaylink.com/knowledgebase/articles/736116-windows-display-properties-identify-numbers-are

Unfortunately this doesn't help the DF monitor profile problem.

I had the same problem as you and I had tried that previously.

I've reached out in my own long post with lots of info and I was hoping to hear that at least someone was taking a look at it or that it was acknowledged as a problem.

How are you connecting your monitors? Mine are through a DisplayLink USB 3 dock. I have the same issue *sometimes* when directly connected to my laptop.

I've had to resort to a workaround that is as unelegant as they come. I manually edited the monitor IDs in the registry for my profile. I swapped the numbers of Monitor1_ID and Monitor 2_ID. The thing is, everytime after I apply the profile, the numbers switch back to the values. So I have to keep swapping them.

I can do either 2 things. Lock the registry key which I haven't tried. The second is I wrote a powershell script to import a registry key with the proper IDs. These are the steps it takes to properly apply a profile (even though DF still reads the numbers wrong, the profile is now correct).

Import registry key
apply monitor profile that extends all 3 monitors
Import registry key again
apply desired monitor profile

Then it works. I spent hours figuring this out. I can't even begin to tell you the frustration. I keep hearing and reading that DF just reads whatever Windows does. Well, it doesn't in all cases. Sometimes it will randomly work out of the blue and all my profiles don't need this crazy workaround, so whatever is happening, I bet it is something the developer can fix. I just wish someone on the support team would reach out and I would gladly provide any information and any testing needed.

They're even located not too far from me, I could send them a USB dock to work on.

I detailed some of what I did in another post: https://www.displayfusion.com/Discussions/View/monitor-profiles-fix/?ID=5cd32989-e5fd-4636-a12e-84c49bf84cfc#1

I considered forcing the monitor IDs in the registry as you have done but for me a few of the programs open on the correct monitor, but most others are on the "wrong" one.

Keith has said there is a program bug: https://www.displayfusion.com/Discussions/View/some-issues-with-programs-opens-in-wrong-monitor/?ID=9f05b02a-d6b4-4a69-b047-73be6e886e1f#15

That was a week ago. Hopefully the next beta will be coming out soon.