You say that this makes it work in AE, is there a way to get Netscript Framework running in AE, or Custom Skills? Curiosity question as I've been waiting for the ability to do this for some time now.
The custom skills framework linked in the requirements doesn't need Netscript framework to function and is compatible with AE. I'm currently playing it on 1.6.640 though this set of texts will be version independent as long as the Glenmoril and Vigilant Custom Skill Mods don't change their text files.
It's not normal. I went and looked to see if the mod's this patch is for updated and they didn't so I'm not sure what would cause it. I did put the instructions on how to make your own version of this patch on the description page so if you take the files from your downloaded mods and convert the format it's a way you could test it. I also saw on VICN's mod page there are instructions to change your skill level by console command if you can't solve it.
I'm not entirely sure if you maybe be able to help with this, but neither skill tree is popping up. Like when I try again access to the trees nothing happens.
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This is what I was referring to, didn't realize it was an additional mod I had installed.