Why won't my iPhone 4 play through my bose sound dock anymore? It used to work, but now it doesn't. It now has iOS 5 on it. (I can't say for sure once iOS 5 went on it stopped working)

When I plug it into the docking station I hear the audio click, the green power light goes on the bose for a second, then it goes off then the phone charges.

If I go into Music and play anything, it appears as though it's playing though there is no sound coming from the sound-dock.

I can connect wirelessly to my Apple TV and it works, though then when playing on the TV, I connected it to the sound-dock and was able to select the "docking station" option (instead of Apple TV)

I've tried the phone on a cheap branded docking station and it works fine.

I've tried an iPod Touch in the sound-dock and it plays music fine.

I've restored the iPhone in case it was some glitch.
But still the problem persists. It charges, and appears to play, but no sound...

Its a SoundDock Series II, and both it and the phone have been powered off/reset to no avail.

Any ideas?
This is a software issue that Apple have not sorted out. I have an iPhone 4S and was prompted to update software on my phone. Since updating I have lost several important functions including the ability to dock the phone in my Bose speakers. Despite Apple support's advice to reinstall the phone, these issues remain.