The setup is a 486 with onboard I/O with Phoenix bios running dos 6.22
I have a 512MB CF card as a second HDD, system boots off its original 300MB HDD.

BIOS correctly detects the CF card in "normal mode" Unable to set the correct heads in LBA mode.
CF card has been tested in another 486 and works fine.

If I bypass the startup files by hitting F5 I can access the CF card just fine.
But if I allow the system to boot normally Fdisk is "unable to access disk 1" and in dos d:\ disappears.

Same happens with either 6.22 or Win98 boot disk, bypass works fine, normal boot unable to access.
c:\ is a clean format /s no autoexec or config.sys exist yet

I'm assuming by bypassing startup I'm remaining in INT 13H or something similar, but in a normal boot dos works in a different mode?
dos definitely works difference between a normal boot or not as bypassing startup also suppresses the date/time prompt.

Is their anyway to keep dos in its initial mode?
This is more just out of interest a side project, I'll definitely be using drive overlay in the final setup.