My guess is that only highlighting the panel (with whatever method we choose) when the panel background is clicked or tabbed-to-- in other words, when it truly has keyboard focus-- would eradicate most of the complaints, since most users will never need to do either of those things in everyday usage.
Ofcource this leaves the issue open for people who select a background color for the panel, or select a background image. They go from 'some color' to bright highlighted grey.. quite a shocking experiance ;-) Was this problem ever thought about when we decided to make the panel highlight?
(ofcource the same is true for the whole applet background color mess, and the window list not using the panel's background color)
-- Chris