I am new to the industry and my thermo is a little rusty, but I have read that it is very important that all the air is removed from the autoclave chamber for the steam sterilization process to work correctly.  In addition, I also have read that air leaks can cause superheating.  Can someone explain this to me or point me to a link that might have additional info on Autoclave operations?

The air acts as an insulating layer.  If it pockets in a particular area of the autoclave, that area will not get to the correct temperature.
As for superheating, I don't believe the air has anything to do with that.  However, when the steam goes from a high pressure to the much lower pressure in the autoclave, superheating is possible.  It is not usually a problem in autoclaves as the superheat level is low and there is usually enough risidual water in the autoclave to quickly desuperheat the steam.  It is a problem in wood drying kilns where the residual superheat reduces the humidity level in the kiln that is important to prevent warping and cracking, but this is another application altogether.

There is a potential for some superheat with a reduction from 45 to 30 psig, however not likely and not very much. Unfortunately I forgot how to read the Mollier chart that will tell us how much potential superheat you could get with this pressure drop.  Even so, any presence of liquid either in the steam or the autclave will quickly desuperheat the steam.
The next question is what are the actual temperatures you are measuring in this top portion (or the bottom).  Is this temperature above that of saturation at 30 psig (274 deg F)?  If it is not, there is little chance of superheat present.
What may be happening is that the steam is condensing on the top portion and subcooled condensate then drips down cooling the lower section a bit.  Or a longshot is that there could be an air pocket at the outlet because the steam trap cannot handle air well.

The sterilizer (autoclave) should have a vacuum pump to draw air out. Check with the manufacturer of your sterilizer and get a copy of its testing & validation procedure. Sterilzation should use saturated steam for full effectivity of sterilzation. Get also their clean steam requiremt and check loads on the clean steam generator. It may not have enough capacity to meet all the loads simultaneously. You can also do a google search on sterilizer cycles, Primus sterilizer models etc.

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