I just finished building a new server for the house here and downloaded the latest build of Ubuntu Server 12.04LTS. My desktop is running an upgraded version of the same (but Desktop, not Server edition). Trying to create a USB boot disk to install on the new box was painfully slow: it was going to take 2.5 days.
After searching all over the web to see what others thought, checking the USB settings in my BIOS, and even rebooting for the sake of a potential fix chalked-up to voodoo, I realized the answer. Checking the USB stick’s partition, it was – unsurprisingly – FAT32. Once I dropped the partition (the stick was brand-new, just opened the package) and created a new ext4 partition in its place, I created my new USB boot disk in 38 seconds. That’s much more like it.