Hello,
So I did the experiment, simply by using fdisk /mbr in the live cd of
freedos. The OS now is not bootable from hdd, and gives read error while
reading drive error. So definitely problem is fdisk /mbr command.

The gotek sees iso images of formatted floppy drives and reads them to a
computer as if it was a floppy drive. It uses the standard floppy
connector, also works on amiga and other non ibm computers. Also almost
everyone who buys one installs custom firmware, that works much better than
default one.

http://www.gotekemulator.com

https://github.com/keirf/FlashFloppy



On Sat, Jun 12, 2021 at 5:44 AM Eric Auer <e.a...@jpberlin.de> wrote:

>
> Hi Andrew,
>
> So apart from the floppy cable problem, you say only
> the Win98 MBR boots correctly, but the FreeDOS one
> will not boot? You have re-formatted the partition
> in DOS (by the way, better use SYS, not FORMAT /S),
> but kept the partitions unchanged, so there could be
> a problem with either FDISK partition edits, or the
> MBR code added by the installer (if any, why does it
> do that by default, by the way?) or of course both?
>
> You could do the following: Use FDISK to backup the
> MBR to a file, then write one of the two built-in MBR
> codes of FDISK and see if that breaks booting. If yes,
> a bug exists in the selected boot code. If no, then
> the bug is probably in the partitioning and less in
> the MBR. After the experiment, you can restore the
> Win98 MBR using FDISK.
>
> I hope that is not too much effort for you. Would
> be good to know whether either of the two MBR in
> our FDISK has bugs. Of course you may have to boot
> from (USB or) CD or floppy to run FDISK for repairs.
>
> Thanks! Regards, Eric
>
> PS: Why would the gotek use ISO to emulate floppy?
> You probably mean floppy images, not CD/DVD images?
>
> > I was able to get both systems working correctly. I first formatted the
> > partition and wrote the mbr in Windows 98. Then in freedos I formatted
> the
> > filesystem and setup system files with format c: /s. I then used the
> > advanced installer to install without overriding the mbr, and after
> > restarting the pentium 2 was able to boot normally, straight from hdd.
>
>
>
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