Hey Jonathan... had the same issue back in the day. Our ruleset was being maintained by an external consulting firm, updated on their system and the files supplied to us to load. Pretty much got-around it by doing the same; created a temp rule set and loaded rules to it. Created "GLOBAL" online and then reassigned all Risks to it - manually. No more problem but a good amount of leg work. By chance were your ruleset files created/updated externally from your system? This occurred back in the SP08 and lower days. Current system - SP14 - we do no have the issue but we also control/maintain our own risks/rulesets. Good luck, let me know if you get an official resolution.
Chris