The version of dfu-util patched to work better on BlackIce II has the disadvantage of flashing more slowly than the original. By accident I've discovered that this can be mitigated by using a larger USB transfer size on the dfu-util command with the -t parameter. On my hardware the maximum that works is -t 4096 for BlackIce II and -t 1920 for the original BlackIce. This results in much quicker flashing than the default transfer size.
For the Arduino IDE, I've added an option to the Tools menu to select the DFU transfer size.
If anyone wants pre-built binaries for the patched dfu-util, the copies used by the Arduino package for each OS platform can be found here.
