Still have a issue with the icons on on the right hand side of the task bar not remaining same color as task bar , back ground colors change to transparent to black back to task bar color again , they do how ever sync with task bar now .
KDE 4.2 latest , Nvidia 180.22 SuSE 11.1
I have somewhat the same problem.
While minimizing/maximizing windows some system tray icons blink.
KDE 4.2 Factory, Nvidia 180.22, OS 11.1
Are you actually on about the sys tray icons, like where kmix and knetworkmanager sit?
I tell you, if so, what you have now is way… better than it was in the early days.
Mine is black background never transparent - but the panel (you call taskbar m$) is transparent. Have you tried different themes ( I use slim-glow), and is it different with and without desktop effects.
caf, I think they’ve deliberately made system tray background dark in newer versions of slim-glow and oxygen themes to hide the ugly icon background issue.
A lot of system tray related issues have been resolved by Qt 4.5 snapshots. I’m waiting for the stable version to come out next month.
Referring to this bug report:
Bug 158094 – system-tray icon backgrounds are not transparent, the blinking icons are caused by a fix. 
See this comment:
Bug 158094 – system-tray icon backgrounds are not transparent.