Mrkol som sa a tie body o tom ze BIOS "vie bootovat len z FAT" je nezmysel, ostatne som necital nechce sa mi to vsetko lustit.
Ak neveris mne, tak si to precitaj rovno od MS, im snad veris:
http://support.microsoft.com/kb/140418/EN-US/

1. Power On Self Test (or POST) initiated by system BIOS and CPU.
2. BIOS determines which device to use as the "boot device."
3. BIOS loads the first physical sector from the boot device into memory and transfers CPU execution to the start of that memory address (to plati pre diskety). If the boot device is a hard drive, the sector loaded in step 3 is the MBR, and the boot process proceeds as follows:

4. MBR code (uz nie BIOS!) loads the boot sector referenced by the partition table for the "active primary partition" into memory and transfers CPU execution to the start of that memory address.

A ani bod 4., ktory uz z BIOSom nema nic spolocne, este nerobi nic s filesystemom. Az bootsektor konkretnej particie (to co spustil bod 4.) obsahuje kod (ktory sa tam nahral pri instalacii OS), ktory sa zaobera filesystemom a subromi v nom a nacita niektore z noch a spusti...

P.S. s bootovanim z USB sticku u NTFS mozu byt problemy v tom, ze OS ktory pouziva NTFS, nerobi pristupy na disk cez BIOS (kde je emulacia USB), a nepochopi preco nevidi HDD, apod., t.j. nezavisi to od filesystemu, ale od konkretneho OS ze co robi ten OS pocas bootovania. Chlapik asi nieco nepochopil.
Taketo problemy sa mozu vyskytnut len u USB alebo u CF pripojenej cez PCMCIA, CF na IDE rozhrani tym ze je na IDE rozhrani nemoze mat takyto problem. Preto som aj pisal vyssie radsej nie cez PCMCIA, tam niektore OS tiez pri bootovani nepochopia preco BIOS vidi nejaky HDD ale samotny OS ziaden HDD nevidi (ak to je cez PCMCIA alebo USB).

... alebo http://support.microsoft.com/?scid=kb%3Ben-us%3B896 528&x=12&y=11 aby si si nemyslel ze to plati len pre FAT