I tried exporting and running an app, didn't do anything special except to load up a working cart and type "export blahblah.bin" and then run the resulting executable from the blahblah.bin/windows/ folder, and the window came up offscreen.
I used some tools and also some estimates to figure out where the app actually came up, and I'm pretty sure it's because I have a rather uncommon desktop arrangement.
Here's an image showing my desktop arrangement from Windows' display settings, with all of the extra info I found/deduced annotated and the position of the exported app when it launches. I hope this helps you figure out where you, e.g. copy/pasted some math and flipped or repeated a coordinate:
(sorry, it's hard to write with a mouse)
Also, just in case it matters, I launched the app from a windows explorer window on the center/primary monitor.
Let me know if I can offer up any more info to help you track this down.
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