Windows moved around after exiting fullscreen SDL app in Windows

I’m reasonably sure this is a problem caused by my app, but I don’t know
why it could be happening. The application is Stella, the multi-platform
Atari 2600 emulator.

I start the app in 640x480 fullscreen mode on a 1400x1050 desktop. The
app starts correctly. Upon exiting, any windows previously on the desktop
are moved such that their lower-right corner is located at the lower-right
corner of the screen. Basically all windows are pushed into the lower-
right area of the screen.

I have other SDL apps that don’t exhibit such behaviour, so it’s probably
something I’ve done. However, I have no idea what it could be. What
could be possibly done in SDL to influence the desktop like this??

This happens both a native systems and in VM, so I think the video
hardware and drivers are irrelevant.

Thanks in advance for any info,