Got the same problem just today (and same workaround).
Hello, I'm sorry for taking so long to answer you.
That is really weird, I thought the problem was solved for good. I'm gonna run some more tests here and reply to you again when I find a solution.
It seems Clickteam Fusion, Itch app and a launcher file don't mix well :(
We updated the game and now the app launches the game directly. The launcher, in case you guys need to configure any settings or buttons, is still available inside the local files.
This is a temporary fix. We'll incorporate an in-game configuration screen in later releases.