Using the GUI to set the color appears to reset the alpha channel to some default value. It is unclear why using the command with only three arguments uses a default for the alpha channel that is different from the default via the GUI.
This issue was already fixed for 1.1: when doing /color it will not be possible to specify custom alpha value, it will be always forced to 128 (0.5) even if provided. Only way to set custom alpha for color will be through lua.
Well … no pressure or anything, but if you release 1.1 with all the 230 fixes and changes in it, we can stop wasting your time by reporting bugs that have been fixed already