Brandon describes the situation correctly.
The subsurfaces are computed in survade UW (or UV) space. Show the wireframe and you will see lines of constant U & W. U is spanwise and is easy to deal with. The tricky part on this one is W.
When doing control surfaces, OpenVSP solves for the W to give the desired control surface length -- it does this at four points along the control surface (endpoints and two intermediate). It then fits a cubic curve (in UW coordinates) along each edge of the control surface.
Under many circumstances, this approximation is not noticeable. However, in situations like yours (where the L/C of the control surface is dramatically different from start to end), it becomes noticable.
The easiest solution is to break the control surface into two (or more) segments in the spanwise direction. This will effectively make the approximation better.
Rob