I hesitated to post because I know how much work goes into designing a theme and that no matter you do somebody will be dissatisfied. But I thought I would share an opinion and please feel free to do with it what you will.
It isn't only the color which makes it jarring, it is perceptual differences in transparency. I am not sure if the transparency levels are different or if the colors just make it seem that way but transitioning from a transparent panel to a nearly opaque blue and back into a transparent area is part of what it makes it feel so drastic.