All what I use is "ent_create" and "ent_createlayer". But, I'm sure they're not the problem
How can you be so sure about that? The ent_createlayer calls are most likely the problem as you can see here:
All .._create and .._remove functions, except for creating and removing level entities, must be executed before the first game_save or game_load call.
Concerning the levels, I meant if you have checkpoints/ save stations like in Metroid or only want to save after a completed level/ mission, then it will be notably easier to implement (using file_ instructions).