Well obviously something has changed.
Was any new software or hardware installed recently?
Was there an update to OSX?
Was Pro Tools or the AxeFX patched?
Have you checked there isn't an issue with the usb cable for the AxeFX?
Do you have another interface you could try patching the AxeFX through?
My band - Ex Curia - Prog metal in an Opeth meets Machine Head kind of way