Why does the pH of this solution rise instead of fall when exposed to the atmosphere? I have a couple of big barrels with a $50\,\mathrm{L}$ demi-water solution of the following nutrients:

$$
\begin{array}{rl}
200~\mathrm{\mu M} &amp; \ce{NH4NO3} &amp; +\\
30~\mathrm{\mu M} &amp; \ce{KCl} &amp; +\\
10~\mathrm{\mu M} &amp; \ce{CaCl2} &amp; +\\
10~\mathrm{\mu M} &amp; \ce{KH2PO4} &amp; +\\
\\
10~\mathrm{\mu M} &amp; \ce{Fe-EDTA} &amp; +\\
\\
0.7~\mathrm{\mu M} &amp; \ce{ZnSO4} &amp; +\\
0.8~\mathrm{\mu M} &amp; \ce{MnCl2} &amp; +\\
0.2~\mathrm{\mu M} &amp; \ce{CuSO4} &amp; +\\
0.8~\mathrm{\mu M} &amp; \ce{H3BO4} &amp; +\\
0.008~\mathrm{\mu M} &amp; \ce{(NH4)6Mo7O24}\\
\end{array}
$$

After mixing those nutrients, I adjust the $\mathrm{pH}$ of the barrels to $5.5$ by carefully adding $\ce{HCl}$ and continuing mixing until the $\mathrm{pH}$ stabilizes at $5.5$.

Then, when I measure the $\mathrm{pH}$in the barrels again after four days, I notice that it has risen to about $5.8$-$5.9$. This is contrary to my expectation. I'd have expected $\ce{CO2}$ from the air to be dissolved in the solution, thus lowering the $\mathrm{pH}$ rather than raising it.

Could someone explain to me what could be happening here?
At that pH, you're well outside the buffering capacity of both phosphate and boric acid, so a $\mathrm{pH}$ rise from $5.5$ to $5.9$ corresponds to a net increase in base of about $2\ \mathrm{\mu M}$.  That implies to me that it's likely something going on with one of the first five ingredients in your recipe, or the $\ce{HCl}$ added to adjust the $\mathrm{pH}$.

I can think of two scenarios:


Similar to Brinn's answer, perhaps a small amount of $\ce{HCl}$ has evaporated out of solution.
If your $\ce{Fe-EDTA}$ was added as $\ce{Fe(II)-EDTA}$, oxidation to $\ce{Fe(III)-EDTA}$ could explain the pH rise, by reducing water to hydrogen gas and hydroxide ion:


  $2\ \ce{Fe(II)-EDTA} \rightarrow 2\ \ce{Fe(III)-EDTA} + 2\ e^-$
  
  $2\ \ce{H2O} + 2\ e^- \rightarrow \ce{H2} + 2\ \ce{OH-}$



I don't know offhand how thermodynamically or kinetically feasible #2 is.  With all of the other metals present in solution, though, it's not unreasonable to imagine that some sort of catalysis might be possible.