I have been programming with an avr usb burner for quite some time. I just recently got the stk-500 to do some high level burning. I was able to use the skt-500 in low voltage mode just fine. I use this guide.
To get high voltage mode working and it reads chips fine but when writing fuse bytes I get "one or more registers differs". In the avr-studio I just changed the interface option to HV instead of ISP. I can't find anything on the net in the matter. I'm able to program the memory just fine.
I notice try to change any of the fuses fail at verification, also the fuses it reads are also not what is on the chip.