This is a known limitation on Windows systems.
For More Information see: http://filemaker.custhelp.com/cgi-bin/filemaker.cfg/php/enduser/std_adp.php?p_faqid=548
This is one of many acknowledged bugs that can be found in the Known Bug List 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
A Google "limit layout folders filemaker"
Link1 is a 2010 thread about the limit in FMP ver11
Moving folders from the bottom to the top of the listing in Manage Layouts results in that folder being displayed properly in the drop-down and other lower folders (that were displaying correctly) "dropping off" the listing. Did some more experimenting with moving things around & it seems to make a difference with the number of sub folders/layouts in the sub folder too. Definitely seems to be a problem with the number of folders/layouts nested...
How do I organize my Layouts in FileMaker Pro?
Answer ID: 7554Last Updated: Sep 19, 2011
There is also a limit in the number of layouts (IIRC around 250). When you hit this limit scrips just won't jump there. If you have 50 folders you might hit the layout limit as well.