iTunes (on the computer) gets updated often, but the onboard software on iPods (that are not iPod touch) does not get updated, except for bug fixes on the most recent models. Since you've owned your iPod "for years," it is unlikely to be something done by Apple, since Apple's iTunes updates do not affect how the iPod operates with the Bose system.
Try "resetting" the Bose system, by disconnecting it from power for at least one minute (to power off completely), then reconnecting it.
Another possibility is the connection point, on the Bose system or on the iPod, being worn out or damaged, and not making proper contact. That is why the iPod thinks it's an unsupported accessory. Visually inspect the connector for damage, corrosion, dust accumulation, and debris (on both sides of the connection).