Don't panic, your new furnace is operating as it's supposed to. To achieve higher efficiencies, new gas furnaces must move more air over the heat exchanger than older furnaces so that as much heat as possible can be sent throughout the house.
The air that comes out of your furnace registers may not seem as warm as the air was from your old furnace, but it will heat your house just as well. In fact, better airflow can improve overall comfort by reducing air temperature differences from the ceiling to the floor throughout your entire home.
Here's a quote from the following website that explains it in a bit more detail
" Some mid- and high-efficiency furnaces offer additional features that provide greater comfort as well as additional energy savings. Furnaces with two-speeds can run on low speed up to 90% of the time, so they operate more quietly than single-speed furnaces.
On lowere speeds, the furnaces will run for a longer time, when it runs. Longer operating periods translate into fewer on/off cycles, fewer drafts and much smaller temperature swings -- only one or two degrees instead of the four-degree swings common with single-speed furnaces. Plus, better air circulation helps prevent your cold feet created by air "stratification" -- warm air rising to the ceiling and cold air settling on the floor. In short, you get consistent, even heat throughout your home.
Variable-capacity furnaces provide the ultimate combination of comfort, efficiency and quiet performance. In addition to the benefits of two-speed furnaces, they offer "smart" motors that can monitor your home's comfort needs and automatically adjust the volume and speed of air to provide the most efficient heating or cooling. They offer added electrical efficiency as well: the "smart" fan motors on today's variable-capacity furnaces use less electricity than a 100-watt light bulb. They operate so efficiently that they can actually increase the efficiency rating of your central air conditioning system and offer you added energy savings when you use continuous fan operation in any season."
http://www.johnbetlem.com/faq.html