I’ll see if I can explain this. When I rotate the arm around the axis that I draw, most of the polys behave as expected, however there is a section of polys that have decided to do the opposite of what the tool is requesting. In the image below I have a blurred mask on the body and I have x symmetry on for both arms to rotate the same. As you can see when I rotate the arm down the shoulder goes up and vice a versa. Does anyone know what is going on?
Furthermore, when I place the transpose tool on the elbow and hold CTRL to create a mask up the arm the mask does not see the arms, it only sees the torso. Please help!
Hmmmm…
Looks like you have the arms and torso as separate objects and not as one contiguous object. To see if this is true, turn on Poly Frame and then do an Auto Groups command under tool palette Polygroups.
What you may find is that the arms and the torso are separate groups.
Though you may have done a Merge Visible under the tool palette Subtools, that command does not create a contiguous object geometry wise, it merely makes the subgroups as one group.
There is an exception though to this and that is using the Merge Visible with the weld option. However, this will only work if the two or more sub tools have identical vertex locations at the seams between sub tools.
So, if it does prove that you do not have one contiguous object, you’ll need to go into the various methods for connecting separate sub tools into one geometrically contiguous object such as retopologizing.
So I know it is one continuous mesh, because I created it in maya. It works fine if I have X symmetry turned off. It seams that maybe the objects center pivot is wrong or something. Yet when I sculpt with X Symmetry, it works fine. I have never seen this happen in the 3 years I have been using z brush. Thanks for the comment though, I appreciate any help I can get on the subject.
REALLY!
I’ll be damned! What the hell is that! HAHAHA! =D
thinks
Could there be a rig in there that you forgot about? Cuz that sure is weird how that elbow joint is popping out when you move it up and the way Zbrush renders I don’t think you’d ever see it.
I don’t use Maya so I’m at my wits end, but I’m sure someone more knowledgeable will come along with an answer shortly. 
It looks like you don’t have a mask on certain areas of the mesh or an uneven mask applied to those areas. Try doing another quick mask and see if the problem is persistent.