By running water down your vents you may have eliminated the possibility of having broken vent lines or vent lines with holes in them. You may want to pull your toilet and install a new wax seal. After a period of time wax seals can wear out and not provide a good seal. A bad seal will not always present itself as a water leak around the base of the toilet.
You may also want to check your toilet closely for cracks that may be allowing sewer gas to escape.
You don’t mention the age of your home or what type of pipe your waste system is constructed of. There is also a possibility of a waste line underfloor having a crack on the top of the pipe allowing sewer gas to escape. This crack may not show itself by running water through the vents. The pipe would have to be filled to overflowing perhaps before the crack would be readily visible. A thorough visual inspection of your waste piping may be in order.
Hope that helps,