I "improved" my program by using as often as possible LabView to let Matlab just do the computation (LV is opening image, reading data sheet and send it as input for Matlab).
And, as you've said, I split my big script into several one which is really better.
Though, the main computation lasts 2min and it s a pity to wait such a long time without being sure of what's happening.
One "solution" is to use a 'STEP' variable which is incremented along the computation under Matlab and use it as an output/indicator for LabView. So, if step didn't reach its max, it means that you can go back to debugging.
An idea for LabView 8.0: create a kind of screen able to receive the standard output of Matlab 😉