arta:
Depending on the size of the HDD that is not being recognized ... a file system check can take a long time (several hours to half a day or longer). Try booting again and letting it just sit there doing the check. The HDD not being recognized may have not unmounted cleanly (and even though you can see it under Linux). If you have them ... look at HDD activity lights to verify NL is doing a file check.
I don't have specifics at my finger tips ... but I believe there are forum posts showing a (complex) set of steps to boot from HDD or CF card, but I'm not sure if this will work with the free version. If you like what NL can do I would recommend purchasing the USB version of 2.0x. (Your mother board, if it does not boot USB may still need a floppy disk to "kick-start" the USB boot process.)

Georg