If it's three different places on the cabin you've used the wrong template, or the wrong UV setting in the def files.

If it's on different parts, like on sideskirts you need to set those in the accessory file, if you're using Mods Studio 2, look for "advanced" paint jobs.
Basically those parts need their own paint job, if they are all one single colour a small 16x16 pixel file is enough, if there's a design on them or text on them obviously they need to be separate.