Thank you for your post.
I am unable to replicate the problem. I double-click a FileMaker Pro 11 database file, but the file never displays as the FileMaker Pro 11 icon is bouncing in the Dock commanding it needs attention. Once I select it, the file loads. I can then use scripts, script manager, buttons, etc. This occurs the same for me on Mac OS X 10.6.4 and Mac OS X 10.5.8.
Please let me know what else to try here to replicate the problem.