You need a qualified CO expert to look at the furnace. Does the new boiler and water heater vent into the same pipe?
You may have a new atmospheric boiler that has a draft hood. You could have such a high draft in the flue pipe which is creating a curtain/eddy effect which is making the boiler spill into the room. Your old boiler had a barometric damper with no draft hood. This made the boiler vent happily up the flue pipe. The fix to your issue would have a qualified CO/Combustion technician get rid of the draft hood and install a barometric damper with a spill switch to the new boiler and water heater.
I would also invest in a low level CO monitor. I would turn your appliances off until then.