I thought V12 are in plane shear stresses and V23 are out of plane shear stresses. So I don't know if they should be the same. Assuming you modeled your pile cap as a flat, horizontal THICK shell element (given your geometry, it would hurt to consider shear deflections, probably wont make too much of a difference), I think you should be looking at V23 and V13. The stress it reports is stress per unit of in plane length.
FYI:
I think SAP will report the shear stress of 1.5*V/A worst case for rectangular sections, which is mechanically correct. But ACI doesn't require this. Play around with your SAP model and see if your getting that.
I highly recommend looking at the CSI website and purchasing "Building Support Structures: Analysis and Design with SAP2000 Software". Very useful for things like this and has information that I couldn't find anywhere online.