Ubuntu Unity is based on Compiz and compiz has never worked completely OK with multiple monitors. Ubuntu does make it significantly more stable and robust to work with multiple monitors, but it cannot cover every possible setup. You're using two GPUs, if you had your monitors on a single GPU, things would be much better.

I think your best bet is to use another desktop environment than Unity (Ubuntu's default), one that does not depend on Compiz. You can try something like XFCE or MATE.

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