It seems that Steam can sometimes have an exclusive lock on the clientregistry.blob file, which keeps anybody else from reading it in just about any way. This is an inconvenience since it means PackBSP cannot read the data it needs about game-assets. I’ve been looking into using JNI with the Microsoft Volume Shadow Service, but not only is it quite a bit out of my comfort zone in C/C++, but there may be licensing issues that would make it very difficult to put the functionality into an open-source project.
It might be easier to lobby Valve for a workaround, like having Steam periodically attempt to dump a copy to some other filename.
In the meantime, simply turn off Steam, start PackBSP, choose the game you want to pack for, and then restart Steam before you reach the actual altering-the-BSP step.