I am assuming that your are using adl to launch the app. NativeProcess API is available only under extendedDesktop profile.You have to run adl in extendedDesktop profile to be able to set the executable and the arguments:
~/sdk/bin/adl -profile extendedDesktop /path/to/application.xml /path/to/rootContent
Did you try the same and still you see this issue?
I added : <supportedProfiles>extendedDesktop</supportedProfiles>And it work! Thanks! :')
Another way to do this is using a command line:
adl -profile extendedDesktop app.xml
Can you give any more details on what you are doing PHP wise and how it works?