A new patch for Atmel Studio 6 (6.0.1843 => 6.0.1863) is now available through the extension manager.
Note: There is also an update to the extension manager available, and I would recommend to download that update first.
Download size: ~23.5MB
The patch fixes the following issues:
DEVXML-310 - Debugging of ATmega32HVB revision E using debugWire does not work.
AVRSV-3545 - Programming UC3 is slow compared to AVR Studio 5.1.
AVRSV-3252 - Atprogram and daisy chain: The order of the daisy chain arguments are reversed.
AVRSV-3544 - Automatic enabling of the debugWire interface fails on devices missing the CKDIV8 fuse.
AVRSV-3492 - Fails to ask the user if she wants to enable debugWIRE and subsequently to enter debug mode.