In the other themes the gradient form header and themed tool strip pretty much shared the same look. However in the Cool Breeze theme there is a big difference. In fact the default color scheme for the themed tool strip is almost exactly the same as the use alternate theme colors selection setting. Is this the way it is suppose to be? 

On the first attached screen shot the main (top) tool strip is using the alternate theme colors. The second tool strip (above the listview) is using the default theme colors. On the other themes the second toolstrip would have the color of the gradient header ("queues" in the screen shot). The second screen shot is the Black Ice theme where the header and tool strip are the same.

Yup, this is correct.  If you don't like the theme, use the new theme editor and create your own theme.  We actually spent a lot of effort on this theme in regards to contrasts, etc. and got people involved that do this for a living (in regards to colors, contrasts, etc.).  This also the point of having more than one theme...if you don't like one, use another

We have it available within our medical app and have had very positive results on this very topic.  The primary complaint of other themes (specifically the Blue Skies) is that there was too much contrast on the alternate theme of the toolstrip.  It was too harsh and difficult to see.  Yeah, there was more visible difference between the alternate and standard settings for the toolstrip background, but that is about the only place.