Do you have all the CS6 updates. What does your CS6 menu Help>System info show as you CS6 version level for example:
Version 13.0 or 13.0.6 or 220.127.116.11 or 13.1.2 here is mine
Adobe Photoshop Version: 13.1.2 (13.1.2 20130105.r.224 2013/01/05:23:00:00) x64
Windows Perpetual should be at version 18.104.22.168 Windows subscription should be 13.1.2
If your version level is 13.0 I saw many Actions and Scripts fail when CS6 updates were not installed. I could not use CS6 till the first CS6 update which took Adobe five mounths to make after releaseing CS6.
it' seems I was running
Adobe Photoshop Version: 13.0 (13.0 20120315.r.428 2012/03/15:21:00:00) x32
Operating System: Windows 7 64-bit
I pressed update and installed update button. I wasn't aware cs6 needed updating since I bought it after cc came out.
Also my OS is 64 bit. Should I be running photoshop at 64 bit? does it matter?
CS6 installer may install both the 32bit and 64bit versions by default.
So I did update my cs6 and opened photoshop CS6 64bit and tried running the ' save layer as file' script. The script worked on two separate files.
I will post back here if it stops working, but for now it looks as if the problem is solved. Thank you so much! This will make my life so much easier!