I have seen various strange interaction effects between MATLAB and window manager systems, most of which I did not fully understand. Some things to check:
- Does MATLAB itself stay responsive (command window, MATLAB desktop GUI)?
- Can you create a figure with uicontrols on it? Do these controls continue to work when SPM controls do not?
- What other programs are running on your desktop? I would look for interferences between e.g. firefox, flash players, libreoffice and MATLAB.
- Are there any traces of things going wrong in the X server logs, e.g. lost events?