Lunar also uses an injection hook on the base game to do what it does, which can interfere with the Game Capture injection hook. Same as MSI Afterburner, Rivatuner, and many shader packs... if you have more than one memory injection on a process, it can fail to find the right injection point due to the new memory offsets. The only reliable workaround is to reload the game, and hope that the injections do not conflict this time. Or use a different capture method.
If having the border and title bar present on a maximized window is the part you dislike, I'd recommend grabbing Borderless Gaming on Steam. It can fullscreen-window games that only have a 'maximize' button, eliminating the top title-bar and window edges. It's pretty cheap, and is great for a LOT of games that make this oversight.
