If you have desktop effects enabled, Ubuntu will "grey out" program windows that it thinks have either crashed or stalled. This can be a useful visual indication that something has gone wrong but the delay before it happens—five seconds—is just too quick. Programs like Synap-tic have a habit of pondering their next action for slightly longer than that, and that can cause them to "grey out".
You can alter the time-out by editing a setting using gconf-editor. Navigate to /apps/compiz/general/allscreens/options and change the ping_delay key to 10000. This will change the "greying out" delay to 10 seconds (10,000ms). For 15 seconds, change the setting to 15000.
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