CasMacC, I chose your post to reply to even though it's rather old now because of one line in particular, the one that makes reference to "suggested the repair would also as an update 'charge' the iPod."
There seem to be multiple issues in this thread as a whole.
1) Devices that are no longer supported by the Bose Dock.
2) Devices that play but won't charge.
3) Devices that will sometimes work if manipulated in a certain way.
I've just had some experience with option 2.
A Bose SoundDock (I think it's a version 1) came in for repair with mechanical damage to the connector. Fortunately the damage was to the outside of the socket, not the contacts, and I was able to straighten it up and now it holds the iPod snugly and the iPod plays. But not for long! To cut a very long story short, I eventually realised the dock was not charging the iPod, an Apple MC688.
The store I'm doing this job for had an abandoned Sounddock repair sitting in their storeroom. I used this to check the iPod and it played AND charged the iPod. Same model dock, same model iPod - in fact exact same iPod. So what changed?
Well, I opened the unit that had been repaired by Bose (2 years ago) and it has a completely reworked 'control' module inside it. This module houses amongst other things, the regulators and 'charge' circuitry. I went a step further and recorded all the voltages on the 24 conductor flat-foil cable linking the module and the PCB holding the iPod. Whilst some of the voltages are identical - in value and pin sequence, others are not! For example pins 24, 23, 22, and 21 are all grounded in version 1. Version 2 sees pin 21 carrying 3.3v. Software cannot do this! Only a hardware change. I also happened to have a control module from a scrap unit, identical in every way to the non-charging unit. It's voltages mirrored the other non-charging unit pin for pin. Now it's possible that both units 'failed' in exactly the same way but, well..., it's less likely.
All this to say it rather looks like iPod 'technology' changed at some point and in the case of the Bose Sounddock, changes were made to support the new 'configuration', for want of a better word.
What can we learn from this? There isn't too much you can do about the hardware side of things. If someone is kind enough to give you an iPod as a present there's always a chance new stuff won't work with old. But firmware....if it works, leave it alone! I've only ever done one OS update on my iPad and it lost a whole chunk of functionality as a result of it. Yes, the buttons do look nicer but I'd rather have full functionality.