Hello! Right, I know what this is, it happens to me all the time, and it's a longstanding issue that I've never managed to get to the bottom of, actually appears in all versions.
What happens is that the controls that are meant to appear in that little dialog get drawn into the main window instead. There is an associated exception report in the console but you won't see that in the standalone version. So on mine at least, if I hit "serial port" and then the window comes up blank, I switch to the "input" tab and look up at the top, I can see the serial port selector controls _underneath_ the main control panel menu buttons. I can usually just about squeeze the mouse in to click one of the check boxes. Which is fortunate if that's the checkbox you want. If it isn't, save the config and restart and hope it behaves better next time.
I'm not sure what prompts it, but it's often fixed by asking it to try a different com port, so it makes me think it's when you're asking for a serial port that isn't in the list. If you can't get into it at all, remember you can edit your default.properties file directly and change the com port there. I can't remember the exact property key, but something like controller.serial.port. Set it to 0 to select "no connection" and try a restart.
good luck!
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