I totally do not mean to insult you with this suggestion, but after you changed the spawn list, either in game or out of game in the text file, did you save it? In game there’s a little disk icon you can click to save it and out of game…well I’ve made changes to those files too and forgot to save before I fired it up. If you did save each time, I wouldn’t know what the problem might be because it’s never come up for me if I’ve saved.
This is an build in function from what i can see. And i haven’t see/found any console commands to disable the automatic finding of extra skins. I guess garry never thought people would want to disable it.