I am working on some framing and getting a new 80/20 geometry, but solidworks seems to treat this extrusion shape differently than previously. 

Previously it would trim the part square and not protrude even when protrusion was on. Which made a nice 90 degree cut.

Now it only protrudes and makes a weird mushroom shape. 

Has anyone come across this? and knows how to prevent it?

On the larger assembly, even when I turn off protrusions it applies them to the other groups. 
This is with protrusion off: