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Well I am happy! This took a few weeks to figure out but it turns out the odd rendering issue with Water (FBO's in general) when not in fullscreen is due to use of ScissorStack glScissors in the Mundus Splitpane classes.
I have edited the classes to NOT perform glScissors on the RenderWidget. This appears to resolve the rendering issue and I am not seeing any negative impacts from the change.
Before fix:
After this fix: