The step by step sequence that I've been using is:
1) plug new flash drive into a linux box (an existing one, or write the linuxcoin ISO to a CD and boot that for this step)
2) find the device name, and unmount it if it automounted.
3) use fdisk to create 2 partitions. Partition 1 is 1GB, type "b" or "c", active. Partition 2 is all remaining space, type 83, not active.
4) use mkfs.ext4 to create a filesystem on partition 2 (probably /dev/sda2 or /dev/sdb2)
5) plug the drive into a windows box
6) go to disk management, format partition 1.
7) use unetbootin to write the ISO
8 ) edit syslinux.cfg
9) remove the flash drive from windows, boot the new box with the drive.
Optional steps if you are doing a lot of boxes:
10) accept the AMD license
11) install ntp
12) copy over my startup and restart scripts (generic versions with CHANGEME as the worker name)
13) shut down, boot from the CD again, and use dd to clone this prepared drive onto other drives
Why do you need to format from windows? Why not use unetbootin from linux also?