If your remote no longer controls your docked iPod:
Remove the iPod or iPhone® from the dock and then redock it. Undock the iPod or iPhone® and wait 60 seconds, then try to redock it to ensure a secure connection to the connector. You may need to try this procedure a few times
Be sure the native audio program is running. An iPod will only pass remote commands to its internal player, not to any third-party application it may be running. Pressing play/pause while streaming audio from Pandora, for example, may cause the iPod to switch over to its own music and start playing
Perform a control console reset:
turn the control console off, then press and hold the console power button for five seconds
when the red led turns off, release the power button and retest the system
Reset the iPod or iPhone. The iPod or iPhone may have malfunctioned and might need to be reset. For more information, visit the Apple Support site
Note: Resetting the iPod will return the Backlight Timer, Brightness, EQ, Shuffle and Repeat functions to their default settings.