I am using SW 2012 and I have done a linear and a non linear anlysis on an assembly. One potential glitch I notice is when I plot P! principle stress. P1 for the linear analysis makes sense to me. Each little vector symbol lines up as you would think with the direction of most tensile stress on the parts in the location showning. Direction changes around holes and features as you would expect Non-linear - not so much! P1 shows all the arrows everywhere in the direction of the X axis, P2 as in the direction of the Y axis and P3 the Z axis. P1 shows just like the normal stresses in the X axis as Sx does. In my case it makes no sense as it is perpendicular to the load. The Vonmises tensor plot does make sense in both nonlinear and linear analysis however.
I think i do remember seeing something like this in my travels. have you checked the solidworks KB yet or spoken with your reseller? I think there was a known issue with the directions of the principal stresses in a sp of 2012 and they may have been fixed in 2013.
can you setup a test example and post it along with some pics of what you're seeing? i could check it in 2013 sp4.0 when it comes out. (i think it comes out shortly, but if not, i can check it in sp3.0)