Some textures are removed on saving map.

[mikebefore]

i know t shis is probably the solution from the same experience. make sure neighboring cube columns are the same texture especially the ones behind the wall you want to paint. also make sure you use the f key to make all the columns behind the area solid. sometimes the g key is hit accidently or previously while mapping and it enables you to make the ceiling and floor different levels and there may be one or many spaces that are tricking the system.