Erratic thermistor readings while using switching power supplies

I put together a solar thermal differential controller that uses a Pro Mini to read two pt1000 sensors and control a relay (more details following). I first powered it with an old linear "7.5v" power supply (actually measures close to 12v), and everything worked perfectly. I then bought a new 9v switching power supply, figuring it would last longer. When I power it with the new supply, my pt1000 readings fluctuate wildly, +/- at least 10 degrees F. My software uses the median of 10 readings to smooth out noise. I've since tried two other switching power supplies, with the same results: big fluctuations that make my controller useless. With the two linear 9-12 v supplies I've tried, there's no problem.

Other details The whole system consists of: An inside unit consisting of two Pro Minis (from SparkFun): one 5v master that reads two pt1000s and two ds18b20s (located in the outside unit) and writes the data to an attached SD card; and a 3.3v slave (communicating via i2c through a logic level converter) that displays readings on a Nokia display. The inside unit is connected via a 20 foot long cat5 cable to an outside box that houses the relay (powered externally) and sensor connections. The switching supplies I've tried are a 9v 600mA one and a 9v 1A one. All power is connected to the raw inputs of both Pro Minis.

Anyone know why the switching supplies would be giving me trouble?

It sounds like the units you have present noise to the circuit. Try a different brand. Look at the o/p with a scope. Use a linear supply. Try filter/decoupling capacitors.

Switching supplies typically output +/-50mV noise on the voltage rail.

The linear reg on the Pro Mini ought to filter that out well, but I suspect its the current noise on your ground wire that's catching you out - you need to fully separate power ground wiring from sensor ground wiring so that no PSU current is flowing along a wire carrying low-level analog signals. You also need to keep those signals well away from the inductor in the SMPS which sprays out interference like a firehose to anything nearby.

Adding some 10uF ceramic caps can't hurt. Extra decoupling on Vin and Vcc both worth trying.