Hi Brad,
I work with infrared camera's and Infrared ray-techs similar to what you reviewed here. To get accurate readings on different surfaces you need to know their emissivity (The % amount of temperature the material emits), The other factors are Reflection and Refraction. There are very few materials that get above 99% emissivity and are generally only used for calibrating cameras. Liquids are generally pretty poor to take accurate temperature readings on because you will get a lot of Reflection from surrounding objects as all objects emit heat, and also refraction through the liquid. So, although you may have got a decently accurate reading from the water you would need to change emissivity once there are bubbles, and different solids to measure off of. You may be able to get a bit more accuracy if you set the emissivity higher (0.90 or so) and only open the lid a bit, just enough to get the gun in and take a reading so that any reflection would be coming off of surfaces that are also reflecting the water/wort. Or just use a common style thermometer as they will be more reliable in this application.