Since I upgraded to 9.0.0.7 my custom folder colors are not sticking.
When I start the program, some or all of them are gone, so I go to Preferences > Folder Colors, click on one of my folders, click OK, and they all come back, and stay for as long the program is running.
There's a known problem in 9007 where the folder colors don't always work in the tree, however they should always work fine in the file display. Is this what you're seeing or is it something more?