This issue is a bug in Ubuntu Netbook Remix. This distribution uses the Maximus Desktop Environment that automatically maximizes windows to utilize more of the small display of netbooks. There is a bug in Maximus where Java Swing windows are not rendered properly. See Ubuntu's bug report here for more information:
To workaround this issue, you can try the following:
1) Unmaximize the MATLAB window:
You can resolve this issue by unmaximizing MATLAB. To do so, double click on the MATLAB title bar in the panel. This bug only affects the program when maximized.
2) Add Swing Windows to the excluded list for Maximus:
1. Open a terminal and type "gconf-editor".
2. Select apps->maximus.
3. Double-click exclude-class key.
4. Click Add and type "sun-awt-X11-XFramePeer" followed by OK.
This will exclude all Swing windows from Maximus which should prevent the bug.
3) Kill Maximus before running MATLAB:
To do so, open a terminal and run the following:
Once Maximus is killed, try running MATLAB again.