I'd have to do some digging on that issue.
A window only has one "size". When the uisettings file is saved, it grabs the actual values from the window. There's no hidden size field, so if the window size is modified I'm not sure what would cause it to not save. It shouldn't matter if it was modified in script or by a user. The only thing I can think of is that the window doesn't think any values have changed, so its not really being saved. Maybe try changing the size with script, then move the window with your mouse so the location changes. This will definitely trigger an update for that window. When you camp and come back I would expect the location is where you left it since you moved it with the mouse, but would the size revert back to the old size, or the new size that you set with script?
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