Basically, I'm running Win 7 x64 Ultimate, and it seems that BWS can't extract the mods after downloading them. I've turned off UAC and PCA, done a fresh install of BG1 and 2 (to D:\Black Isle...), patched them, done a quicksave for both, ejected the CDs and downloaded all the mods via BWS. The only thing that is non-standard is that I've had to manually get BPSeries v4.00 and edit the relevant component in BWS (ie renaming and changing bytesize) since v3.61 is no longer available. I did this for an 8.3 install in Win XP, and it worked, so I don't think that's the problem.
As you can see from the log, I'm getting a weird extraction problem. Does anyone know of a way around this? I tried extracting everything manually, but that seems like a fools errand; the paths were all messed up.