There was a bug (#165285) that caused subdirectories of the application directory to always have the names transformed to lowercase when installed. This bug was introduced in version 8.1 and was fixed in version 2009.
Because the bug only affected subdirectories of the application directory, you can avoid this bug by setting the application directory to another arbitrary, dummy directory in your distribution. The downside of this workaround is that when the installer is run, the user will be able to change that the path to that dummy directory, instead of the root directory of your application. To avoid confusion, you might want to disable that directory selection page of the installer. To do so, you must manually change the value of "SingleDirectory" in the distribution's setup.ini file (right next to the setup.exe file) from 1 to 0.
Let me know if you have any trouble.
Mert A.
National Instruments