Just a question, you said you measured an opaque cup of water, but how exactly?
One thing I learned a few years ago about IR thermometers, is that they're a bit colour-dependent. We were trying to measure the temperature of a heatsink (we had some big RF transistors to cool), and pointing at the silver gave a massively different reading to the black (we couldn't use a thermocouple reliably because the RF interference made it read a few hundred degrees). In the end the conclusion was (by testing on various other non-RF heat sources) that pointing the IR at a black spot (even a bit of black texta on the silver heatsink was enough) was the only accurate way of measuring.
So by extension, to measure temp of chemicals, I'd be putting the liquids in a black beaker or something, letting the temperatures settle for a few minutes (most important, because you're still probably going to be measuring the temp of the container, not the chemicals), then point the IR thermometer vertically through the liquid to the bottom of the beaker.
Or just use an immersible (mercury, digital, whatever) thermometer, still probably more accurate...