The problem is exactly what you stated...backdrafting. The mechanical draft furnace vent needs to be above the water heater vent. When properly configured, the water heater will draft properly by being drawn by the mechanical draft, not a secondary outlet for the furnace as currently and improperly installed.

The proper configuration can be found in the appendix of the gas code. It needs to be changed as it is a code violation as well as a CO hazard.

Dead men tell no lies. I saved a family's life many years ago who had an improperly vented water heater. Their basement had 3,000 times the max CO limit when the gas co arrived...and they just thought they were overly tired from a hard days work.