Hi Fice
I've seen this plenty with both KDE and Fluxbox (no flaming please, it's just a fact). You can get apps to load and they may not necessarily make it in to the system tray and it seems to be that they are loaded in to memory before KDE has finished it's start up routine to handle the system tray.
Probably the best bet is to use the script like you do now, but put a 5 or 10 second sleep at the start of it. It's all I can think of at the moment.
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