I was having this very problem. The formatting of the DataObjectManager fields was messed up until I refreshed with ?flush=1. It was isolated to one page which was heavily laden with extra tabs filled with DOM functionality.
The fix for me turned out to be an empty line above the opening php tag <?php on an unrelated custom page class. A tricky bugger to find, but once I removed the empty line so the php block opened on line 1 the system was happy.