HVAC furnance runs for awhile, stops for 2 minutes, then starts back up and continues to heat until set point reached

I have a Carrier 58GS150 system. At night it is set to 69. In the morning it is set to 72. Recently, I replaced the air filter. The system starts up fine in the morning and tries to reach 72. Being that it is very cold outside, this takes some time. Mid-way, the whole system will shut down for 2 minutes. It will then start back up and continue to heat into order to reach 72. Sometimes one shut down is enough, sometimes it takes 2. I don’t think that I noticed this shut-down issue with the "dirty" filter. Any ideas what is happening??