To clarify, is it ok to put the battery in when its off and closed with the charger in? Because thats what I did, I didn't put the battery in and out while powered on with the charger.
There is no off when the DC jack is plugged in, if the Pandora was powered off and you plug in a DC or USB power source it will turn on and boot up.. and if you shut off the Pandora when a power source is plugged in, it will just turn back on.. This is essentially how all mobile devices work, except the Pandora lacks a lower power charging boot mode.. Like on a phone where you are not quite fully booted into the OS and you just see a battery charging image or animation. But really this doesn't make a difference, because the potential for damage could still happen even if it was in an off state.
So it could potentially be an issue, but it sounded like you were having issues prior to this so it's hard to say if this scenario really damaged it or not. If you had access to a voltmeter to check the battery or the charger.. I would be curious about getting a current measurement when it's plugged into the charger, but that isn't an easy thing to setup if you are not experienced doing so.