Signet of Illusion does not recharge shatter skills (F1, F2, F3) (F4 is not considered a shatter skill, but seems like it is) when activated while using Chronomancer.
Tested today in Armistice Bastion.
F4 is a shatter skill but has an explicit statement clarifying that it can't have its CD reset by other mesmer skills. That said, you are right about F1,F2, and F3 not resetting when they should. I assume it has something to do with the pointers in the code for Signet of Illusions not being updated to cover both base mesmer shatters and chronomancer shatters.