Okay.. so here I am searching for the solution for this weird problem! Seeing none of the other answers working for me, I did the random most thing I could think of and it worked.
Open SceneBuilder (a brand new one). Go to File > Open Recent > Clear Menu. Close Scene Builder.
Now the bug should be fixed (it did for me)
PS: I am ashamed of posting this answer. But since this is a nasty bug which wasted time, I don’t want anyone else to waste theirs’.
PPS: Also, I can’t double-check this solution, since it worked for me and I can’t recreate the buggy scenario anymore.