Hey Angela, 

It is best to look at the tray temps on the screen before you pull the food out so you can know a quantitative number for the tray temps. 

In general, if the tray temps have not reached full temperature then the pressure is no being reached, either because the recipe is set too low on the pressure, there is a leak in the door gasket, or the pump needs an oil change or some sort of service. 

The freeze dryer operates such that it will only heat the trays to sublimate enough water to reach the set pressure. The pressure you see on the screen can be thought of as water molecules floating around in the chamber. If the trays only have to be heated to 40F to reach 800mtorr, then they are only going to heat to 40F. If there the pressure is set too low, if there is a leak, or if the pump cannot pull a deep enough vacuum then it will not reach final shelf temp. 

You can do an ultimate vacuum test to see the health of the vacuum pump, you can do a leak rate test to see if there are any leaks, or you can just bump up the pressure on the recipe 200mtorr or so. 

Thanks 

Brent