I'm having similar problems for about the last 20 builds with the gradient color settings in spectrum Analyzer. They seem to get scrambled when saving with Vis Studio. I've found a work around that might help in your situation.
I've been editing the .mjv file with a text editor and as soon as I set the values in the file they update in Media Center and stay set like they should.
Vis Studio seems to be unsupported (and maybe unloved) but I could not live without it for music playback.
Good Luck
Rick