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I switched to MO after playing several saves using NMM. I heard a lot of good things about MO so I decided to give it a whirl.

I've figured out most of the features but I'm still a little nooby at the software when it comes to troubleshooting conflicts and problems such as the ones below. 

 

I have two problems:

- What do they mean? What would be causing them? How do I fix them? Thanks for your help. *If any other information is needed like screenshots of Data folder or .ini files let me know and I'll add them.

 

#1

"There are files in your overwrite mod - no guided fix" in problems panel. There is not other description for this issue in the dialogue box. 

 

#2 

This message when loading into the game and starting a new save (Would this be caused by installing SKSE in the Skyrim folder NOT through MO?)
 

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https://linustechtips.com/topic/597221-mod-organizer-help-skyrim/
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Double clicking on the overwrite folder will open it up and show you what is inside it.  Usually you have to take what is in the overwrite folder and move its contents into another folder, OR right click on the overwrite folder a select create mod, depending on whats going on naturally.  The overwrite folder is eff'ing awesome, though I'm sure it doesn't seem so at the moment.

 

Been a long time since I first installed SKSE so I don't recall all the steps, but SKSE IS supposed to be installed outside of MO.  But I would do what your screen shot tells you to do tbh.  Go to your skyrim folder (where you where supposed to have installed skse) then "data\SKSE" and open SKSE.ini in notepad and look for:

 

[memory]

ScrapHeapSizeMB= XXX
DefaultHeapInitialAllocMB=768

 

And add it if needed.  Though I wouldn't be surprised if your inside your overwrite folder is an SKSE file.

 

The -forcesteamloader (including the minus) is something that can be added to the argument field for the SKSE launcher within MO when you configure the executable.

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