Thank you for your post.
I have been unable to replicate this issue with FileMaker Pro 13.0v3 running under Mac OS X 10.10 (Yosemite). Does this occur with all of your long scripts? Does this occur with every database file?
I would like to see a clone of your database file with the script in question so I can try it here. Check your Inbox at the top of this page for instructions where to send the file.