So I have been having this issue for way too long and I cannot fix it for the life of it. The number of times I have scrapped This room and rebuilt due to issues is ridiculous. Anyways this is the problem.
Problem: I make the brushes needed and then rotate them to match the rotation of the wall. After working on this for awhile
I save and exit radiant. The very next time I go on radiant
it screws up all the brushes that were rotated. I have tried 2 different ways to rotate it like the "Independent Arbitrary Rotate Tool", manually rotating it in the viewer and rotating it in the grid. I use a mixture of the 3 and have tried to save it different ways.
Here's a video on Google drive to demonstrate on what is going on:https://drive.google.com/file/d/0BwFZ1zVn6pkGNUh3eUxlbndhUk0/view?usp=sharing