Just thought I'd mention that I am experiencing the exact same problem. I can no longer access the Branding Editor correctly when logged in to CPanel as the reseller.
All I see on the page is:
Available Branding Styles
Currently Selected Style: [root]
If a cPanel user does not choose a style, he or she will use: [root]
However if I manually enter the URL in my address bar, it works:
(the reseller username is "branding" in this particular instance)
I also want to add that I am having tremendous problems integrating new icons into my new theme. I have successfully added icons using the web tool you are offering on your site but it does not offer me all the necessary flexibility so have tried configuring them manually using the .conf files. The categories and category contents appear just fine, but the graphical icons do not! Despite having uploaded the png files to both the reseller theme directory as well as the root theme directory and running the sprites script repeatedly. Am very stuck.
EDIT: Turns out I was editing the x3 theme directly. Copied the changes into its own style folder within the x3 folder in my reseller cpanel account. While the Branding Editor still did not work within that style, switching styles back to root then allows me to work with the Branding Editor as expected (don't think this is intended to work this way, so there seems to be something up for this). Also, running the sprite script from within the cPanel branding editor (there's a link at the bottom) seems to have activated my icons in the cpanel, whereas previously running the command line script as root did not.