First of all, you need a link to the MAX6655 datasheet.
Here you go.
I'm repeating myself, but...
If that flux is still on there you definitely need to remove it. It's a leakage path and the amount of leakage will vary with humidity. Look at the "Remote Temperature Error vs. PC Board Resistance" curves. Major bad news. Also depending on which pin(s) the leakage path 'connects' to, the signal leaking in may vary depending on what the processor is doing.
Flush it with isopropyl to remove the flux. Depending on how long it's been on there, you might need to brush or scrape at it. A toothpick would work to scrub the flux off.
According to the specs, (in particular the "Remote Temperature Error vs. Common Mode Noise Frequency" graph) the setup should not be very sensitive to common mode frequency below 1 MHz. I'd be somewhat surprised if there is much signal coming from the magnetic stirrer that is above 1 MHz, but it's hard to say considering the somewhat chaotic motion those things undergo. In any case, if there is a common mode noise issue with the stirrer, those ferrite beads and the amorphous metal cores I sent should help dramatically. Just slide them over the shielded twisted pair cable. (Even if high frequency common mode noise is not an issue with the stirrer, it will be with the CPU running.)
Differential mode noise is more likely a problem with the stirrer. The 'loop' between where the red and white wires exit the gray jacket of the cable, and connect to the diode pins will be prone to injecting differential mode noise into the measurement. The red and white wire should be kept twisted together as tightly as is practical. It looks like the red wire is longer. If you don't want to redo the soldering to tighten the loop up, I'd suggest at least folding the red wire back on itself to minimize the loop.
The resistance of the connections is not that important because you will be calibrating out its effect with the Digitec. The issues above are substantially more important, because they involve things that can change the calibration of the system.
I design electronic instrumentation. I've been burned by all these issues multiple times. I hope you won't be.