Can Apple update the firmware on a Made for iPod device using the iPhone? I have a Phillips alarm clock with iPod dock and an iPhone 4. When I got the iPhone 4 first, when i docked it with the alaram clock, i got an message on the screen of the iPhone saying that "This accessory is not designed to work with the iPhone and may cause interference", but after the upgrade to iOS5, this message does not occur. I did notice with iOS4 that interference would happen when playing music on the iPhone, but now it does  not seem to happen... 

And it started to make me think: How did my device "learn" to play nicely with the iPhone 4? Was it the iPhone that was tweaked? and either way, can Apple push down updates to these devices? I know thats a lot of devices, but could it happen?
The accessory has to meet very strict design requirements from Apple to connect on the 30Pin connector. And the approval requires to work with the latest version of iOS. Due to this, the earlier versions of iOS may give you some error messages in some conditions.

Not having seen your accessory, I would take a guess it would be due to the resistors that are connected to the USB D+/D- lines if it is only a charge only device (or) the authentication chip would be the latest version 2C