I noticed two things started happening after upgrading my ipod photo to 3.6.
1. Sometimes when turning it on, I get the apple battery with a lightning bolt through it icon, which requires a hard reboot. This was a consistent issue for most of rockbox's life, but had been fixed in 3.5. I've had the same thing happen on 3.6 when plugging the usb cable in to put new music on.
2. When playing music, about half the time, the selected theme disappears (I personally use DGT curled leaf). I'll look down 10 minutes later or so, and the theme will be back, but something is causing it to not consistently display. This has never happened on the menu screens, strictly when playing music.
If you need any more detail, or I can be of any more assistance, please let me know.