I have to make a couple of disclaimers.
1. I am not sure I understand what you are describing.
2. I didn't use Win98 much, and I have not used it recently.
That being said, it
sounds like the trouble might be related to file assocations.
Under Windows 98, MS-DOS is actually an executable file called command.com.
You may need to remove the file association for .com files.
Removing a File Association under Windows 98
1. Click Start, point to Settings, click Folder Options, and then click the File Types tab.
2. In the Registered file types list, click the file type or file extension that you want to remove, and then click Remove.
For more information, read
How to Create a File Association in Windows 98.