kal,

Got your file, and I think I've figured out the problem. The rotation interpolation of your shoulder control curves is currently set to Synchronized Quaternion. A quaternion rotation automatically calculates the smoothest interpolation between keyframes using an invisible 4th curve instead of tangents (a quaternion is a 4-dimensional complex number). To gain access to tangent handles, you need to change the rotation interpolation to Independent Euler (Graph Editor | Curves | Change Rotation Interp). It looks like some of your other controls are set the same way. One thing you should also check is the Default Rotation Interpolation for new curves in Preferences | Keys. It's entirely possible that you have it set to Synchronized Quaternion as a default instead of the more familiar Independent Euler.

This should thoroughly confuse any n00b who stumbles into this thread...