If you're using the FN full install you should have no problems, as it's built around that resolution.
But if for example you're using select files in a an otherwise default install, they're going to be odd because they use a different size, like you said.
You'll notice that eq2ui.xml contains this bit on the first line for a fetish install:
ScrollExtent="1280,1024" Size="1280,1024"
The windows have to match that or else things go weird with scaling and such.
As for why Zonx uses 1280x1024 here... I'm not sure, so I'll leave that up to him to answer =)
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