So, I like colouring guns and clothes with the GECK, but there appears to be an issue. I can change the colour of guns and hats as I want, but when I try to color clothes (tested on Sheriff's Duster and BoS Power Armor) the whole jacket/armor/cloth disappears. What's the problem here, it would be really cool to make clothes like you want

You have an invalid normal map is the usual culprit for that issue.
How are you applying your texture to the clothing?