Same here, tho I get more than just blank spaces and weird GTK icons. When KDE first initializes, systray gets drawn in two rows and looks terrible - only icon that's recognizable is KPowersave rest of them (by default - Keyboard Layout Switcher, Klipper and KMix) are all drawn either one over the other, or strangely stretched, palette spoofed and rest of the area is full of strange artefacts. There are also random blank spaces. At that stage, when I start a new app that uses systray, for example Pidgin, aMSN, LinuxDC++ and so - it gets even worse - systray becomes pretty much useless.
The only workaround I have found so far is to remove systray widget, then re-add it again. In 90% cases it fixes it, if it doesn't - I do the procedure again. Very frustrating but so far that's the only way to fix it. There are some problems with that as well - it tends to loose some icons when re-initializing, usually aMSN is the one that doesn't show up after re-initialization. Also, sometimes aMSN systray icon shows up as a regular application in taskbar with name 'si'.
And remove-add procedure wont help with Pidgin icon - it will still look messed up. However, sometimes that icon turns normal (after being `stretched`), but it's pretty much random and I'm not clear why and when it happens.