From Eclair to Foyo even with out charging you get a warning (on POST) that these batteries are not supported. So what happens, the phone and car dock will not charge the non OE batteries.
You have to carry around the charge plate/brick to charge any and all of your used batteries. Works fine for me, the charger is small enough to fit in a jacket or backpack.
I have not tried long term non OE battery in my car dock for USB audio, to see what happens. I would rather use the 3.5mm in that case. Or swap back to your OE battery for charge and audio.
I show my three batteries to all my iphone friends and laugh.
Edit:
To be clear I heeded the warnings and have never tried, short of the first time, to charge the non OE batteries in the car dock or with the wall / PC charger. When I use the non OE batteries I bring the provided charger.