What could be causing noisy pH measurements?
Several factors may influence your sensor readings:


Electromagnetic noise. However, since EMF should be directly proportional to pH, it seems to be not your case. If it were the main reason, the same amount of noise would show up in both the nutrient and the storage solutions.
Temperature. I've included this one because it is unclear from your post whether you are measuring the actual solution temperature when you calculate pH from EMF, or just assume that the temperature is some constant value. The Nernst equation may be used to estimate the amount of "noise" (i.e. the difference in EMF) one may expect from the temperature fluctuations: $\Delta E=2.303\frac{R\Delta T}{F}pH$. That is, if we can neglect the temperature dependence of pH itself, i.e. when $\Delta T$ is relatively small (when $\Delta T$ is large we can no longer neglect the temperature dependences of equilibrium constants). If, for some reason, the daily temperature change in the nutrient bath is different than that in the storage solution, you may expect to get slightly different readings.
Math. We should not forget that the value measured (pH) is logarithmic, and that it is the concentration (well, activity) of protons that makes the difference. For example, to change pH from 6.45 to 6.05 (±0.2), you need to add just around $5.4\cdot 10^{-7}$ mol/l of protons, but to change it from 4.26 to 4.24 (±0.01) - $2.6\cdot 10^{-6}$, or almost 5 times as much. In other words, the same actual $[\textrm{H}^{+}]$ fluctuations cause different pH changes around different pH values. In turn, these $[\textrm{H}^{+}]$ fluctuations may be due to slight inhomogeneities of the nutrient solution, differences in dissolved carbon dioxide concentration, etc. The more neutral your solution is, the more sensitive, with respect to $\Delta [\textrm{H}^{+}]$, your pH electrode becomes. In this regard, you may want to prepare a few solutions with different pH and try to investigate the noise vs. pH dependence. Or do something even more simple - as a reference system, instead of the storage solution (which, in addition, probably possesses some buffer characteristics), try to use something more neutral, like water, and see if the noise is as large as in the nutrient solution.


Since my analytical chemistry is a bit rusty, no other potential cause comes to mind.