I'm no expert at all but sometime ago I remember reading something about problems with SCP in dual core systems.
OTOH, why don't you update to latest official version (3.6.7. media_vp's, 3.6.7. exes and 5.3 launcher)? Or even to beta 3.6.8.?
For latest oficial builds and vps:
http://scp.indiegames.us/news.phpFor latest and current builds, (they're beta but usually pretty stable), see "Recent Builds" >> "CVS Builds" (Sorry I don't know how to insert the link to the forums).
For beta media_vp 3.6.8., see "The Freespace Upgrade Project" forum.
Please notice that 3.6.8. media_vp's and latest exes are not compatible with previous versions (3.6.7. or older).
If the problem is caused by dual core crash you can try setting Processor Affinity for the fs_open.exe. (I had this problem with RegCleaner 4.3 and my HyperThreading P4). The process to follow is very well explained in
TweakGuides Tweaking Companion Version 3.0 guide. You can obtain it in
http://www.tweakguides.com/TGTC.html, and you only need the regular and free version. The process involves using
ImageCFG.exe (a Windows NT utility) that you can download from
http://www.robpol86.com/Pages/imagecfg.php. Read the Guide for step by step process or even the ImageCFG download web.