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Far as I know it's not a problem with SKSE unless you installed a mod that made changes to how the game runs that uses SKSE, ie Engine Fixes. You can run Skyrim Launcher not SKSE launcher and the first menu that comes up should have the options for window mode if it's check just uncheck it close down skyrim then run it with SKSE and see if that fixed it if not you'll be basically disabling mods and reactivating them one at a time to see what is causing this.
NB i'm going to assume since you have SKSE installed that you've modded your game one of the ,mods usually installed durning the early stages is One Tweak and may be the culprit behind why your getting Borderless Window mode. also when you run SKSE it doesn't give access to the menu you get when running the skyrim launcher when you run SKSE it runs the executable TESV.exe the only visual you have that skyrim is running is a black window follow by a blank screen that switches to the in game menu. (it may or may not also show the screen with the smoke and chanting.