energy minimisation can be essentially chaotic, tiny differences in the potential energy surface / initial conditions etc can rapidly lead you to minimise to different minima, especially if you start from very high energy structures. I think the 'bug' in your set up is that you start from a very high energy state and then minimize. If you did this for many different starting positions you should locate all the possible minima eventually. But better to start from close to a local minima and not ask so much from the optimiser.
It is not really a question of one being right and the other wrong in this case if you find different minima. Do both minima exist for both 1200 and 1400 Ry cutoff with consistent energy differences?
HTH,
Matt