The filter that gets changed often is to clean the air that gets blown back into the house. Yours may be so clogged that the burner is running to the time limit without putting enough warm air into your house. You do need to change that to reduce dust in the ducts and house. It is a simple procedure in most furnaces.
If your system has not been serviced in a while you should definitely schedule that ASAP. At best, a dirty burner is less efficient. More seriously is the chance your flue is clogged (as suggested above.) This will eventually lead to a buildup of carbon dioxide and carbon monoxide, both of which are dangerous.
When you come inside and feel your lungs become irritated you are probably feeling the CO2 buildup. You will not feel the CO but that is more dangerous because it displaces and blocks oxygen abortion on your red blood cells.
Don't wait. Call today for service. Also, people who burn fuel in their homes should have at least on carbon monoxide alarm.
Good luck!
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