Twine (Sugarcube 2) has stopped creating new passages with new links. Is there a simple solution?

Basically, when I type standard links into a passage eg [[linkylinky]] and [[linky2]], twine sometimes will only creae one passage, and sometimes will create neither. If I manually create the passage, it then links them. Have I done something weird with a setting somewhere? Should I uninstall and reinstall? Would love some advice if anyone recognises this problem.

Twine 2, Sugarcube 2, Linux version (running on Mint).