Why is my startup script getting a timeout error in FrameMaker?

Using FM 11

ExtendScript

Windows 7

I'm running an ExtendScript from the FM Startup directory, by starting FM from a batch file. The Extendscript opens multiple book files (one at a time) and does a save as pdf for each one. FrameMaker terminates the script with a timeout error at random points in the script after only one or two saves. The Extendscript runs fine when I run it from the FM Scripting window. It only times out when I run it as a startup script. Is there some workaround for this? Sadly, I find no documentation about this.