I think the OP actually manually paused BWS at some point, but (I don't know if you are aware of this), you can order a pre-emptive pause when you are choosing your mods in BWS. Just find SCS, right click, and choose "Pause before the mod", and then continue as you see fit. It might just be that pausing the BWS for a moment before mods that heavily modify files (tweaks, BP, SCS) will be enough to solve the problem (ie. Out of Memory actually means Out of Memory). I recall having a similar problem when installing a megamod on a machine that was more than enough for BG2, but evidently underpowered for BWS with SCS.