I had a similar problem: a very long delay when I first ran avrdude before it started to do anything. I had to actually patch avrdude to fix it. Arduino 0009 (which should come out tomorrow) will include the patched version and a "Burn Bootloader" command.
I submitted a bug to avrdude: AVR Downloader/UploaDEr - Bugs: bug #19882, Many "error in USB... [Savannah] but haven't heard anything. You might want to add a comment explaining your experience (with the long delay on startup). These things sometimes get fixed faster if multiple people report them.
OK, will do ... but back to my question about the time it took to burn and to verify the flash, 51 seconds and 512 seconds .... is that right? 512 seems awfully long!
cheers ... BBR