I found the problem, well, not one actually :D, and what is really funny is that none of them is related to this thread.
Actually this issue exists because of the conflicting changes to the tech tree.
My mod changing tech tree in the way that you need to research quality module technologies to unlock qualities:
quality-module1 -> normal+
quality-module2 -> uncommon and uncommon+
quality-module3 -> rare and rare+
Aditionally i changed the prerequisite for epic quality technology from quality module 1 to quality module 3
Changes made by author of upcycler are hiding quality module 2 and quality module 3 technologies so you can't unlock new qualities with my mod
So looks like our mods just can't work together without adapting
Upd: Looks like if you change property "Disable modules with quality" to false in settings, it could work