Ok, I found some patches with the Valleys1-3 simulators and they do indeed overload something in X2.
So I fixed them, saved them, and they now behave.
However, this is only for Bank F whose progams are stored in
Shared DXi\Pentagon I\rgcaudio Pentagon I\Presets
I've searched everywhere and I can't find the programs for Banks A-E.
In Bank A there is, for example, a program called Evolving II that also uses the Valleys simulator, but I can't find where it is located to save the new version on top of.
There doesn't seem to be a generic "save" function that'll just update the patch, wherever it is. Well, there is one at the top left beside the red X, but it doesn't do anything as far as I can tell.