Thank you for the post.
I am unable to replicate. To attempt to replicate, I performed the following steps:
1. Opened two .fmp12 files with FileMaker Pro 13.0v3 Advanced
2. Pressed ⌘-`
3. Pressed ⌘-`
I tested both Mac OS X 10.8.5 and Mac OS X 10.9.4. With both operating systems the application switches back and forth between the database windows.
Please let me know if I am missing a step to replicate.
It's not doing it now. I don't know why it was acting that way before. Except that the machine does not have as much RAM as I'd like (but it will by the end of the day.)