Unfortunately a clean reinstall didn't do much. However, I spent some time working on the issue, and trying other ways to reproduce it. It sometimes happens if I open two windows and then close the inactive one, in this case two maximised notepad2, but it works with a few different applications so far.
1. Open notepad2.exe and maximise.
2. Open another notepad2.exe, which auto-combines with the first window.
3. Close the inactive tab, and then the primary tab will minimize.
There's a few issues with maximised windows. Sometimes they simply don't merge. Like cmd.exe windows. If I leave one open, force a merge, each subsequent window will then merge, but initially, I have to drag and drop.
Also, some windows will have their tab bar outside the screen space, whether maximised or minimised. I need to use the taskbar to minimise/maximise to see the tab bar.
Oddly, explorer.exe windows seem to suffer none of these problems. It's like all testing was done on getting them to work perfectly lol. Well, except for the fact the quick access toolbar vanishes if I use a combined titlebar.