I did unfortunately (well, fortunately for me) not encounter anything similar, can't say that I would know what may cause it.
From what you describe the loading process is definitely slowed down by something, but there are a lot of possible culprits. If you have an antivirus, you can try to disable it temporarily to check if it changes something (and then add an exception for the game afterward). Same if some kind of anticheat or other process scanning live apps are running on your computer.
You also have the standard possibility of your graphical drivers not being up to date (unlikely to make a difference for this game, but you never know sometimes).
The issue could also simply be related to optimization or some kind of incompatibility with ClickTeam Fusion, but in this case not much you could do on your end :/
Hope you'll be able to find a solution or that a patch may help you down the line!
