Thanks for posting!
I was able to replicate the behavior you've described so I went ahead and forwarded your post to our Development and Quality Assurance departments for further investigation. I should also note that this appears to reproducible on OS X as well. Unfortunately, at the moment, I don't see a workaround for this issue beyond using a FileMaker Pro client to run the script.
One way to use FileMaker client for this, is to use a FileMaker File as a "robot file". A system task scheduler can be set to open the Filemaker file. A script set to run when this file opens can then perform the export script in the hosted file.