If you really are booting from a raw DOS floppy with no Config.sys or Autoexec.bat, then the problem can only be MoBo. Raw DOS loads in conventional memory unless you specify extended Memory (< 1MB) with HIMEM.SYS, EMM386.EXE and UMB etc.
Of course, DOS won't reconise long file names or NTFS/FAT32 file structures etc. Furthermore, loading a display driver that wants to run in high memory, but you haven't specified it in Config.Sys, will lead to difficulties.
Perhaps you try the old trick of pressing F5 when the text "starting MS-DOS..." appears during a DOS boot to by-pass the config.sys and Autoexec.bat files.
Again, sorry if this is Granny/Eggs territory, and it may not all be strictly accurate anyway, but we're all getting desperate out here!