If it was ok before the filter change it is probably the filter not sealing and allowing air to be drawn in,if it is the type with the thumb screw type clamp,fill the filter with fuel push it HARD up into holder and clamp it up it should feel rock solid when clamped.I fitted a filter from a large car part outlet and had loads of trouble in the end I put the rubber seal off the old filter on and it worked a treat,the new filter seal was slightly thicker and wasn't allowing the filter to pull up properly.It has stopped because you ran it with the fuel in the filter only and it hasn't drawn more fuel in as it is sucking air.
Rich
April 2008