I think I've found the culprit. Auto-Ghost was turned on because the first time I followed the guide I was exceeding the plugin limit by using most of the user recommended mods in the guide, and advice outside of the guide told me I could only make a bashed patch merging these plugins if I enabled Auto-Ghost. Opening Wrye Flash without creating a bashed patch moved all the .ghost files made by this to overwrite. The log I am about to post shows this. Attempting this again caused the ESMs/ESPs to be sent to overwrite as well, despite the fact that I did nothing different. I will send the logs for each of these in a separate post as attempting to post them with this caused me to lose what I had written.
Edit: it turns out I am not going to be able to post my logs because every time I click post a loading sign comes up for a while and then nothing happens. I'm going to mark this as solved though, because it seems I've found the problem. If the root problem of exceeding my plugin limit reoccurs I'll make a different post. Thanks for your time.
