It's a bit old thread, but I encountered very similar problem with my ipod today.
When installing bootloader I get "Error reading partition table - possibly not an Ipod". However I was able to install Rockbox firmware without a problem. I have an Ipod 5G (Video) 60GB. I have tried restoring it in iTines, but it hasn't helped.
My iPod just has been repaired - it has the motherboard replaced with the one from Ipod 5G, but 80GB (not my original 60GB). I don't know if it can have something to do with the bootloader installation problem but I thought it's worth mentioning.
Any help would be very appreciated!