Loading time complications

I've been working on a particular game for a ridiculously long time, now, and in it, I have several sub-apps taking over with a pause menu and an inventory menu.

As I test the game in the runtime editor, these sub-apps seem to function properly. However, when I build the .exe to see if the game works on anyone else's computer, there's a ridiculously noticeable load time when going into these sub-apps, and in some cases, going in and out of the sub-apps alters timer-based events I have in the game.

Does anyone know what's going on with this? Though I have absolutely no problem re-arranging the game to not need these sub-apps, I do want to know what the deal is at least.