When things don't work... just walk away.
Someone else reported the issue this morning (with FM Pro9.0v3), he rebooted a couple of times, got frustrated and waited until we got to the office (there is 4 hour difference between our offices). By the time we talked, he did not have the issue anymore.
It gave me the idea that maybe all it was, the CPU was not available after the update, not allowing FileMaker to display properly.
I re-installed the patch on my PC, waited for Rtvscan.exe to be done, all is good again.
As it happens, the problem is still unresolved for some users: the FileMaker screen does not display properly, even after having waited... or it works for a while and next time they go to FileMaker, the problem re-occurs.
one user stumbled on this unlikely solution:
Use Ctrl-Alt-Del (to get Windows security dialog box) and then simply Cancel: the FileMaker screen and all its elements are back!
I know, it is not supposed to make any difference, but it does. Why? beats me.