Glad you got it sorted. This happens when the window is just maximized, not fullscreen? I already have code that takes Spine out of fullscreen when the file dialog is shown and restores it after. For me, the file dialog is always on top of the Spine window if not fullscreen. Hmm, do you have your taskbar set to auto hide?
Edit: Yup, seems auto hiding the taskbar makes maximize identical to fullscreen, so the file-dialog-behind-Spine-when-fullscreen problem occurs even when Spine thinks it is only maximized. I've changed it so Spine temporarily comes out of both maximize and fullscreen when a file dialog is shown, then returns to its previous state afterward. This is in v1.2.8 which is building and will be available in 10 minutes.