Hi,
I am playing the mod together with Space Exploration (0.6.128) and I did not notice an issue with Space Exploration recipes.
I just verified that my biochemical facility producing cryonite crystals does indeed have +100% productivity (cf. https://i.imgur.com/rYsoIGO.png) and correctly produces 2 crystals every cycle, whereas the normal output according to the recipe is 1 per cycle.
Can you please provide a screenshot of the same properties window, of an affected facility of yours? Especially the blue text is important, so that I can judge which other mods may affect this.