When it successfully detects the serial port, does it say what IRQ and I/O port?
This is just speculation but I wonder if part of the configuration that normally goes in the BIOS is actually on the HD, or alternatively, if whatever is on the old HD is filling in some info in RAM that DOS uses to figure out where the serial ports are. If interested, there are ways to dig into this with the DEBUG command if I or someone looks up the addresses (BIOS data area, etc.)

Well, when it is recognised it is seen as com1 with the standars IRQ for COM1, there is somethng i can do to give you more information ?

I mean the i/o port in addition to IRQ.

Try this, both with the original hdd and the replacement one.

Run the DOS debug command
at the - prompt type: d 40:00
The first two bytes dumped should be F8 03.
To get out of the - prompt just type q

It will be interesting if the result differs depending on which hard drive you use.

Ok, i've done it if i follow the procedure you suggested, with the original segate hdd i have F8 03 when executing the debug BUT with the other hdd with a clean dos 6.22 installation if i execute the same debug commands i got 00 00 instead of F8 03 ... so something is happening in this segate ...

Yes, weird. I wonder if the BIOS settings are stored in the boot sector rather than in CMOS or something. DEBUG also has an e command you can use to overwrite things in memory. You could try to use that to write an F8 at 40:00 and an 03 at 40:01 and then exit and run msd. Even if this works, it's only until rebooting.

By doing that, IT WORKS, msd see the com1 port correctly, i issued those commands : -e 40:00 F8 ; -e 40:01 03 and after that the port is recognised correctly, so maybe can we create a little bat file that do it at boot ? Maybe i can insert it in the AUTOEXEC file ? Another thing is that if i connect the original segate hdd to a pc it is not recognised so it is possible that there is a partition in the hdd that is used to store bios configuration or something toshiba proprietary, cause i'm unable to dump the original hdd

Debug will read from stdin if you want to do it that way. I'm surprised no one has chimed in about this though, you'd think if all Toshibas of this model worked this way it would be widely known.