@jriofrio some bioses can lock out 'unapproved' pci cards,i could guess there could be some kind of lockout for cf cards,so maybe trying the original (with verified backup)
as for autoexec.bat,that is something that dos starts after boot (since you are headless - no keyboard/monitor),this would work if it boots but don't show serial,there would be commands exactly as you type them manually...but hard to debug if you don't see anything,it could be asking for bios file,or wrong switch or telling bad command and you never know...so if you are certain what to type with paths,you can try this,i bet there is switch to 'reset/reboot' after flashing,probably cmos clear parameter too,so you could wait for console (can't restart while flashing still works,so you need to be sure you can reset or wait long enough)
edit:cf cards also have some modes of operation(udma,pio),so maybe it just can't talk correctly to that asmedia sata bridge(asmedia are not that great,sensitive to firmware versions-talking from experience with theirs usb-sata bridges,i don't trust them),so best could be sticking to the original..maybe even adding floppy image as image to grub,that could work,but requires a bit of linux/booting knowledge,i think there must be some loader too,not sure
edit2:i finally looked at your image(sorry,too much up,didn't read it all),when it boots,you should see it there i believe,this kinda looks like it is really not booting,so getting into grub seems like great idea,maybe allowing editing for starters...(need to do in grub.cfg probably on cf /boot/grub.cfg or menu.lst)