Try deleting both "Main Window Layout" and "Main Window Position" under the following registry key, it should reset all the FME window positions to default values:
HKEY_CURRENT_USER\Software\Safe Software Inc.\FME Workbench\Window States
I recommend making a backup first...
The best way is keep trying to dock it in the right spot by hoovering the window over that spot.
Ultimately, if you can not get that to work, you can revert to the default settings for your windows by removing the setting in the registry that stores this information:

But that is certainly your last option and not recommended.
Thanks @david_r and @erik_jan I removed those registry keys and all my windows are back to normal.
I was trying to dock it as bottom pane by hoovering the window there without success, and this worked for me:
First dock the windows somewhere else (left or right column)
Then, from there, dock it as bottom pane by hoovering the window over that spot
In my situation: doesn’t work from “flying”-window to bottom pane, but works from left-docked windows to bottom pane