LAST EDITED ON Aug-07-02 AT 11:39 AM (EDT)
Most of the various versions of DOS for WIN9X have a slightly different version of command.com. Somehow, you've managed to get the io.sys startup file to look for a different version of DOS than the one expected in the registry initialization. You probably installed some software that's looking for a different DOS version than the one io.sys calls. WIN98 stores several backup versions of command.com in various folders, including the root directory of the HD, and the C:\Windows directory.
Roboot into a "true" DOS prompt and type <ver> (without brackets) to see what version DOS says is there. Then boot back into WIN98 and check the Device Manager information to see if you have the same version as the DOS prompt.
As Larry suggests, the first strategy is to make a fresh Emergency Startup Disk from your current version of WIN98. You can use this ESD to boot to the command prompt and use the command <sys.com a: c:> (without the brackets) to attempt to restore a compatible version of command.com.
Another strategy is to open the system information utility, then use the "Tools" menu to open the system file checker. In the system file checker, check the radio button that says "Scan for altered files." Then click the "Settings..." button in the lower right.
On the "Search criteria" tab include (as a minimum) the following directories: C:\ and C:\windows. The defaults will probably be OK. Then run a system file check to see if you have any altered files. Have your WIN98 installation disk handy in case you need to extract any replacement files. System file checker may or may not catch a command.com compatibility error if you're still using any 16-bit software or drivers.