I couldn't find any other full solutions so I thought I would post mine. This may be a bit of a hack, but it resolved the issue to the above problem:
public void login(HttpServletRequest request, String userName, String password)
{
UsernamePasswordAuthenticationToken authRequest = new UsernamePasswordAuthenticationToken(userName, password);
// Authenticate the user
Authentication authentication = authenticationManager.authenticate(authRequest);
SecurityContext securityContext = SecurityContextHolder.getContext();
securityContext.setAuthentication(authentication);
// Create a new session and add the security context.
HttpSession session = request.getSession(true);
session.setAttribute("SPRING_SECURITY_CONTEXT", securityContext);
}