So I am now having this same exact problem. I did grab the standalone theme and uploaded it to my host. This resolved the color picker showing up issue, but I am unable to make any changes I make there 'stick'. I have changed 'presentation' to 'design', but each time I select my colors and choose "Save Custom Colors", the defaults revert back. I have deleted and uploaded the theme several times, thinking that I've jacked something up with my tweaking.
Is there any chance that I need to upload a color palette to my hosted file structure, or are these colors standard codes among the development realm? I did check and the files are NOT read-only.
I started out with this theme at http://www.pelokee.com and absolutely love it as it appears there - darker blue in the header basically. I am trying to mimic that theme at my hosted WP.org site at http://www.theappiagroup.com/ but am stuck with the lighter blue default colors that I don't particularly care for.
Thanks in advance for any info....
Pelokee