KDE 4.8.0 upgrade - application icons not showing in system tray

I updated to KDE 4.8.0 through pacman yesterday, and I noticed that system tray is not working as it should. Icons for some applications do not show, while other work OK.
For example, Akregator icon appers in tray, while icons for Skype, AppSet or the Java application I'm developing do not. I notced that notification ballons for these apps pop up at upper left corner, instead of lower right.
Anybody got some idea what might be wrong? Maybe QT version issues?
One more question: how can I bring up these application windows when they do not show in tray?

When you click on the arrow do they show up in the list ? that list is for hidden apps, if they are right click configure and see here http://userbase.kde.org/images.userbase … ings-2.png

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