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DOS Boot up Disc

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I have a computer running Win 2000. To run certain programs I need to boot it up into DOS and I have a DOS Boot-up disc. Of course it only allows me to boot up into the A:/ drive. I understand that.
My question is this:- What is the difference between booting up using the DOS boot-up disc and re-formatting the HD and installing, say, DOS 6.22. Some of my old DOS-based programs will run on an old computer that has DOS 6.22 installed as the operating system. Indeed they will also run on other computers using Win 95 or 98 where there is, I believe, a true underlying DOS system. So what am I losing by booting up my Win 2000 computer using the DOS bootup disc?
All comments welcome
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Well could be numerous things.... for one is the hard drive that has windows 2000 on it in fat32 or is it NTFS. IF it is NTFS, dos boot disk in general will not see it. Also you have to configure dos, the boot disk may not be loading everything your dos program needs to run...

So without more details it's hard to say what problems you could run into.... are you actually having errors trying to run something?
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If you need a DOS OS on a seperate computer try FreeDOS. You could also make dual boot with DOS on a second partition. That can be done with Digtal Dolly.
Resize and format the second partition in FAT16 if you do. You should not need any more than 1 gb of hard drivve space. You could even do it from a USB flash drive.
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