I fixed it! 
What I did was I exported my database to .sql (not necessary if you plan to start from scratch), backed up all of my custom quests, deleted the "lua_modules" and "quests" folder and then reran the installer. 
It replaced the quests/lua_modules folders and now the lua quests are working. 
It also reset my database, but since I had exported it to sql, I just imported it back in. I also replaced all my custom quests. 
 
I guess it installed wrong the first time, or maybe I messed something up on accident. Either way, I got it fixed and thanks @Huppy for pointing me in the right direction. 
 
I wanted to leave the fix here on the forums just in case anyone else had this problem. 
		
	
		
		
		
		
		
		
		
		
		
	
		
		
	
	
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