This is a problem with the RPG Maker engine. If the amount of icons exceeds a certain number (somewhere in the 4000 range) it will show them all as black boxes. You'll have to reduce the amount of icons you have in one iconset.png file to under 4000.
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Hey Brother. I've been watching your videos and following your work for a year now. And while the content may not be what's popular right now, you are a pioneer in this field. I really appreciate you. I haven't seen you upload anything recent (probably because I'm focused on rpg maker content) but you are keeping it alive. Idk what you're into these days buy don't quit. My rpg is a small piece to a bigger puzzle. It's no where near finished but I owe you a lot. I do still need a lot of help but I'm getting through it. If there is anything I can help you with feel free to reach back out. Otherwise I'm watching dude. Keep it up.