I just received Alix boards from PCEngines. I did not have the chance to put my hand on these, for working problems, but I thint that what I made can help you in creating a boot CF image. I did not work with freedos, as I had an old floppy bootdisk from W98, but if freedos uses the same file names...
I work with Windows XP
I put the DOS floppy on A: and a CF (8MB) on my USB writer
Downloaded SP27608.exe from HP and executed it (it is a USB format tool from HP)
The resulting CF sometimes is only readable when you dismount&mount.
When I see at the CF in exlorer everything looks good.
Tomorrow I hope I can try it.
Hope that helps.