I had similar problem with "synergy" and have seen reports about other programs. As a work-around I installed "lxpanel", configured it to only show the system-tray, located it so it doesn't interfere with the KDE panel, and made it unobtrusive. Any panel should work, I only used lxpanel because I was familiar with it and it is light-weight.
I understand KDE changed the way they handle system-tray items. Either they need to make a way to use the "old method" or all the effected programs will need to adjust to the KDE method. Don't know how that is going to go!