AFAIK, running with the MTU at 1400 should not cause any issues. Your box will have to work slightly harder, but unless you hardware is already running near capacity, it shouldn't be a problem. Ideally, you could get the equipment that is causing the issue fixed and set the MTU back, but this is not always possible. I would trace the route and do some tests. With more specific information, it might be easier to get your ISP to investigate. As for the remote sites, they should be fine with their default MTUs.