It might be to do with the resonating properties of your ukulele. I have a Kala concert which can sound a bit harsh on open 0003 C chords. It has quite a different tone colour from other chords. It's great for songs in C, where you got this WHUMP on the I chord, but not so great in G, where G is a bit weak (being in 2nd inversion in 1st position on a ukulele) and the IV has this WHUMP.
Sound is a complicated creature, and every body in which sound vibrates "likes" particular sounds. Every instrument, most every room. The best ones "like" lots of sounds. It has to do with distances between reflecting surfaces, how parallel they are.
As southcoastukes suggests, try different strings. Strings resonate different harmonics differently, and some might be weak on those partials.
For recording, what you really want is a notch filter, which is like a precisely aimed EQ which can cut the level of just that frequency. They're on some acoustic amps, and are quite common in recording software.
Hope that helps!