Home Layout: Rooms that are built over a garage will always be cooler in the winter months. Does your home have multiple levels? If so, the air flow will take longer to circulate throughout your home.
Seasonal: Rooms with several windows will always have a warmer temperature. A rooms temperature will change depending on the time of day. For example, rooms that face east side will be warmer during sunrise, and rooms facing the west side will be warmer during sun set during the winter months.
Equipment: Your air conditioner or furnace might not be the right size for your home which will give you inefficient heating and cooling. You could have blocked or closed air vents or even improper duct work. Where is your thermostat located? In its location, is it affected by drafts, the sun or other heat sources? This would prevent it from reading the true temperature in your home.