MATLAB: Matlab timer doesnt work in stand alone application

MATLAB Compilertimer

Hi Guys,
i have built this application that listens to a certain folder and continuously checks if certain files appear in it. once these files appear i activate another function to process them. I implemented the folder listener using a Timer object with a fixed rate of 30 sec. (i.e – every 30 sec it should check the content of the folder.) Everything works great when i run the code from within Matlab, yet when i compile and then deploy the app the timer only executes once and then exits the program.
any idea what can cause this difference between compiled and un-compiled versions?
system is Ubuntu 14.04,
timer object instance:
myTimer = timer('TimerFcn',@checkFolderForChanges,'Period',h.listenerInterval,'ExecutionMode','fixedSpacing','BusyMode','queue','UserData',userData);
compile arguments:
mcc -mv fileWatch.m
debug lines i added to monitor the timer, from within Maltab:
timer running mode: on
timer tasksExecuted mode: 682
timer running mode: on
timer tasksExecuted mode: 683
stand alone deployed version (exits after 1 timer task execution:
timer running mode: on
timer tasksExecuted mode: 1
vncuser@mathlab:~/visualizer$