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Disk at C: Not capable of booting itself.
The Startup floppy disk is essentially a bare bones DOS 7.x system disk with various disk initialization tools, such as FDISK.EXE, FORMAT.COM, and SYS.COM. These tools allow you to initialize the hard disk prior to the Win 98 installation.
Using the Alternative Boot Disk: This diskette allows you to boot into Win9x where the system disk at C: is not capable of booting itself. This is usually a result of the partition that is assigned to C: is not an "Active" DOS Primary partition.
How to Format the hard disk in msdos?
format disk /parameter
Example:
format c: /s will format disk C and make it a system drive.
If your Startup Disk does not have the Format.com, you can download it from:
http://www.allbootdisks.com/disk_contents/download/98.html
After formatting, your non-removable disk (hard disk) at c: will have one program installed and that is COMMAND.COM
Your computer will now boot on drive C: and ready for installation of windows