Yeah, there's definitely some flakiness restoring windows/widget sizes regarding the F&R window being open, and whether or not the application is maximized or not. And as you noticed, closing F&R before closing Sigil is the easiest way to avoid most of it altogether.
It's been on my todo list for a while. One of the easiest fixes I could probably make to alleviate the problem is to simply not save/restore the open/closed state of the F&R widget at all (i.e. always open Sigil with F&R hidden). But I hesitate to do that until I've exhausted all other options.
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