Gotta say this is a cool mod, however I partially ran into the same issue as Junior.
So most of the scripts I installed are inside the scripts folder while a few others such as ModLoader, SkyUI, Mobile Style Loading etc. are in the root directory. Once I installed MoonLoader, SkyUI couldn't find GInput anymore, even though it was installed. I moved GInput in the root directory and game worked fine at the menu, however once I started a new game, it was loading like the vanilla game, even though I have the Mobile Style Loading mod installed.
This made me realize that the scripts folder is apparently ignored when using this mod. I tried moving the mod's asi and the folder inside the scripts folder, along GInput, and this partially fixed my issue, however only a few mods were actually loaded, which I belive they are the ones that are loaded prior to this mod (SkyUI loaded, meaning that GInput loaded, which is loaded before this mod, however SkyGFX and SilentPatch weren't, which are loaded after this mod). Moonloader's scripts however worked fine (tested the BetterSkybox mod which uses Moonloader now)
Is it possible to make this mod less location dependent?
It's actually moonloader that is causing that,not letting asis from /script to be loaded.
Moving every asi to root folder fixes the loading for me.(Idk about asis in /modloader though, I usually don't put them there)