Sharkbit,
As you mention you never have had any problems with either SP2 OR SP3 this brings into play the possibility of a conflict between either my graphics card,SP2 or Catalyst driver,or a combination of all 3.Finding the culprit is going to be easier now because the last time I was playing SH3 I was using default XP Home Edition and not SP2 and this glitch was not there.
My card is an aging Radeon X800 Pro (old I know

,but its still a good performer in most games up to about 2007 or 2008) I have ample memory (2GB) and use a page file of 4GB,even though most of that is not needed.
Can I just ask what card YOU have ?