Parenthesis indicates that the file has been opened as a "hidden" file.
There's a bug in FileMaker 11 (anybody know if it still exists in 12?) that results in very inconsistant listing of open files in the windows menu on Windows systems. Files that are open simply aren't always listed in the Windows menu.
What's really suprising about this bug is that I can define an unstored calculation field that uses the WindowNames function to list all open FileMaker windows and it always lists every open, nonhidden FileMaker window. I've even set one up with an OnObjectEnter script trigger so that I can select an open window from the list by clicking into this calculation field...
For More Information see: FileMaker Window Menu fails to list all open files
This is one of many acknowledged bugs that can be found in the Known Bug List thread here in the Report an Issue section of the forum.
It can also be downloaded as a database file from: http://www.4shared.com/file/8orL8apk/FMP_Bugs.html
"Parenthesis indicates that the file has been opened as a "hidden" file." To the best of my knowledge, I've never seen this in FM11 (but I seem to remember that in earlier versions). Files are either listed under the Window menu, or had to be displayed by selecting 'Show Window >'. Well, there you are now: every day is a school day for me.
I also never had any problem with seeing all open windows listed under 'Window' (up to the limit, after which I had to click 'More Windows...', or somesuch) but in the last 6 months I have noticed more and more of our installations under XP and Win7 showing only a random, small, selection of what I know are the open windows. When I (for example) select the file name I want from 'Open Recent' it immediately brings the 'missing' window to the fore. No wait, no password: it is clearly already open.
Because it used to work (as far as I know) and now it doesn't, I suspected a Windows update was the instrument of change.
It's not. I've had the behavior you describe (and use the open recent option as a work around) since early in the release history of Filemaker 11. It's fairly random and FileMaker has had difficulty replicating it so you may have just been lucky to avoid noticing the problem till now...
have you been able to write a script as a workaround to get the window list back?
I've already described the only work around I've come up with in this area--an unstored calculation field that lists all open windows.