This is a known issue with some versions of FIleMaker.
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: https://www.dropbox.com/s/jt09b82i0xijbu3/FMP%20Bugs.zip
Thanks for the information about the "known Bug". If it would be helpful, I can get this to happen EVERY TIME. so let me know how I can help pin this " but" to the wall.
You are welcome to add your comments to those already present in the original report thread. What version of FileMaker and OS are you using? I can't get this to occur in FileMaker 12 or 11--just 10.
Also, check the Show sub menu in the windows menu. If the file is opened "hidden" (minimized on windows) it will be listed in that sub menu.
im using fma pro 11 v3 on a Lenovo T500 windows 7. As you can see from the pics, the file is not opened hidden, and drops off when I click on a script button to perform a simple go to script (also enclosed). It does it every time.. I can make it reappear by restarting. Clicking on any other file is ok, just the go to "invoices" script from the Checks file. I can send you whatever you might want so you can recreate the problem to kill this bug. I have done a work-around so it's no longer a problem for me.
I am just a fellow user. I can't kill any bugs nor will sending me the file help accomplish that in any way. You'll need to use Report an Issue to bring this to the attention of the TS people that actually work for Filemaker Inc.
But since this problem does not appear to happen in FileMaker 12, they probably consider this bug as already dead.