In PowerPoint's color menu pop-ups (Fill Color for example) there are 2 rows of color swatches.  The first row shows the colors in your color scheme for the current presentation.  They do not change unless you change the color scheme.  The second row are recently used colors and they cycle.  Every time you select a new color, the color is placed on this row and an 'older' one is deleted.

 

If you use Pick Color to select any color, that color is placed in the recently used colors row and can be selected the next time you wish to use that color.