I've admittedly used only a few of the Ultimate Branding features and they seem to work except for the Login Image section.
I add a photo it looks like it is saved but stays on the WordPress logo and never changes.
If it matters I used the standalone Login Image plugin with the same image before I installed Ultimate Branding and that worked fine. The standalone plugin is currently disabled in the network.
I should probably also mention that I am running the Multi-DB Plugin with the 256 setup. Just in case it is one of those plugins that needs special instructions and I missed it.