I'm a new user of ME and just installed ME 2006. I can not make any changes in color settings. Regardless of my choice of color template, colors on the screen do not change...
Where are you "choosing" the template? Extension setup? If you are just editing a color template, you have to hit the save button or the changes are only in effect for the current session.
Using 2006.02 I went to Tools-Customize-Filename Extensions
I selected one of the extensions I had a file loaded for. Changed the color template (Colors) to something new (Light Blue Background) and obvious and pressed the OK.
I was promted to reset extension configuration for currently loaded files - pressed OK and finished closing out the dialogs.
Colors changed just fine. Is this what you are doing to change the template?