Finally fixed it after going through it with support. Basically did everything I had done before again in the order:
Restored EISY from a previous ISY994i backup (again).
Restored PLM (again)
Ran the File: Restore devices (again).
That fixed everything after I reconnected all the wireless devices.
All, I did so more troubleshooting and the programs run that a re triggered by time etc. However, the programs by an event from a device will not. For example a switch that if double clicked, turns on another light.
Thanks DennisC, I tried all that and nothing worked. I noticed that if I run the "then" on the programs, they work. Looking at the event viewer, it seems that the eisy is not seeing an event coming from the switches, i'll try restoring the PLM.
I completed my migration from an isy994 to eisy. Devices are linked and controllable, amazon talks to them ok, but no programs will run including new test ones I create. Any ideas? Thanks.