Hi,
From the trace screenshot (with a single call to DrawWindows) it seems like the window has somehow been added to the SlateWindows array twice. We track windows via FSlateWindowHelper::ArrangeWindowToFront but we always remove the incoming window before (re)adding it. Do you have any engine modifications that might affect this, or any code that directly interacts with the SWindow? It looks like this is your main window (and not something like a tooltip), correct?
If you want to attach the full trace, I can take a look to see if anything stands out that might cause this. Does it still occur if you toggle global invalidation?
Another idea would be to set Slate.VerifyParentChildRelationship and see if it trips in your development build.
Best,
Cody