I have two home - both with ISY-99i Pro. I have had the same symptoms at both. Things work for months, I leave and come back to a blinking red error LED. I finally debugged one of the devices at one house and decided it was a bad SD card (after combing your great forum). I put in a new 512MB SD card and upgrades to latest firmware the restored my ISY settings from a backup. All appears well.
What can I do to not have SD card issues? In my other devices I do not have SD issues.
P.S. The SD card I pulled out of my ISY when the error light was blinking was readable in my PC SD card slot and only 8MB of the 128MB card was used