I think I've narrowed the issue to an old problem discussed in the archived thread viewtopic.php?t=8650&f=3
It looks like this problem has reared its ugly head again. I'm getting an Application not Running error -600 from any external script I execute. I can temporarily stop the error by repairing disk permissions but it comes back eventually or sooner if I restart the server. Reinstalling Indigo did not help. Starting IndigoServer from the finder was temporarily helping but not any more. Other actions may stop the error temporarily too but I have not gotten a good handle on this, and nothing fixes it permanently. I really miss this function since I use Applescripts from the Messages app to allow Siri to control Indigo.
The timeout error was probably related to the fact I was calling Indigo multiple times in the script.
I'm using Indigo 6.018 and OS 10.10.
--Dave