I haven't noticed the "blinking clock" behavior and I don't use seamonkey. Can you elaborate on what you mean when you say the clock is blinking? I have both KDE3 and KDE4 installed and haven't noticed any issues with it other than the seconds lagging sometimes under load.
If you want to take a screenshot, use the "Snapshot Delay" feature in KSnapshot. Give yourself enough time to setup your desktop to where the problem arises, then it should snap it just as it is.
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