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I've got the problem as dxhall and his description of the system matches what I have. I still cannot understand why the check valves are installed/omitted on bikes with a similar system, it just makes no sense (Calli Vs Spiney), unless it's possibly connected to he difference in frame volume (Tonti Vs Spine)
May not be your problem, but to quote you "a banjo bolt on top of the spine just behind the steering head, which once held a hose that went to the air box". I would be thinking that if this hose were missing, you would not be getting the negative pressure required for the breather setup to function. I ran into this on Triumph that was seething oil - hooked up the airbox suction hose like the stock setup had been and it was all better.
It wont change anything. Vented to the filter or vented to the atmosphere is the same pressure wise. It would be a good idea to run it to the filter though, as grit could get sucked into the breather box without a filter.