FYI.
With both FM 11 & 12 saving a Structured Application via the Structured Application Designer leaves the structapps.fm file (%appdata%\Adobe\FrameMaker\[11|12]) with invalid structure, if the element RulesSearchPaths is present. I have reported this to Adobe as bug #3943816.
The scenario is most probably unlikely as most of the time an application would use the default search paths for rules. I have chosen to use the element due to the previously reported entity mapping errors (see Incorrect entity mapping in FrameMaker 11 and 12 - A FYI!). I have placed screen snaps of the before and after to illustrate the problem.
The scenario is the same for applications in the Global Application Definitions, i.e adding a RulesSearchPaths will cause the global structapps.fm file to have invalid structure if the Structured Application Designer is used to Save the application.
An important note is that is not necessary to make changes to the structured application definitions in ether scenario. Why the Save or Save As buttons are active when there have been no changes made is another question, probably linked to the prompt to save changes, when none have been made, when either Edit Application Definitions or Edit Global Application Definitions are clicked.
Jon