Oh wait! I just looked at you screen shot and know what is going on. The boolean join worked but random faces in the model disappeared. I have seen this, and it started with maya 2011 for me. Not saying it's a bug as it could also be associated with the graphics card.

1. reassign the shader to the surface. Another common new behavior that started in maya 2011 for me is the tool works but maya just randomly loses the shader attachment for random polygons in the surface. Without show border edges on I cannot tell if you have lost the polys or just the shader attachment. But as you are having to use fill hole you definitely are losing polys. You can grab all the edges in the model and hit fill hol but if some of the holes are adjacent then you'll have incomplete edge loops.

2. When you do an operation and faces get deleted I find there is only 2 solutions. One use fill hole and or append to polygon to rebuild the geometry or if it is just to many faces that go missing. You will have to attach the parts manually and not use the boolean until if or when autodesk fixes this bug (if it's a maya bug).

Sorry for all the extra info above but it is handy to have a set of the rules and fixes for maya booleans.