First of all, that is not a WaterFurnace problem that is an installation problem. It sounds like you have issues with your ducting, because if your ducting is to small or to large for a zone it will cause issues. It also sounds like your intellizone panel may not have been setup properly which is also an installation issue and not a WaterFurnace issue.
Their explanation of emergency heat kicking in could be if the system is not able to heat the zone then it could kick on and it could not heat the zone if the ducting is to small or if the Intellizone setup was not properly done.
It sounds like you need to have a chat with your installer and how they sized your ductwork because you even mentioned "constricted ducts" which is not a WaterFurnace issue.
For more help please reply back with your model number(should start with NSV/SDV/NVV/NDV) of equipment and what thermostats you have.