The game seems to favor loading the Volkur shipset's designs. One possibility would be that it is because they are alphabetically the latter of the two (V as opposed to G), or perhaps the script governs that part of the loading process as well. I suspect it's the former; a brief examination of the script doesn't seem to reveal any obvious explanation as to why it would specifically focus on Volkur.
In other words, changing the first differentiating character (for example, the first differentiating character between 'Volkur' and 'Voldur' is 'k/d', which is also the only difference, as well as the only one that matters with alphabetical sorting) of your shipset folders' names to something alphabetically following the appropriate Volkur character should fix the issue. (For example, data/designs/hyperdrive/Exa could be changed to data/designs/hyperdrive/Wexa, Xolkur, Volqur or whatever you like, so long as the difference is significant enough to change the order in which they're loaded.)