That sounds weird to me, could you send an image of 1) what the game screen looks like after opening up the Encyclopedia scene AND 2) what the console says after this issue occurs (To view the console, press F8 while playing, then switch to the console tab at the top of the window that opens up)
I am not sure why that would be happening, especially if there is no error in the console. It does not happen in my test project. Could you reproduce the issue in a blank project using only CGMZ Core and Encyclopedia and send that blank project to me via discord DM so I can look at what might be happening?