OK, the reality of life. 95% of DOS programs that worked in Win 95 work in Win 98, however the DOS in Win 98 is NOT a full DOS and not all the DOS commands and processes are supported in the standard Win 98 cut back version of DOS.
The default format setting for Win 98 is FAT 32, many DOS programs working through Win 95 and Win 98 have no problem with this as the Win 9x o/s usually gets the file and then feeds it to the DOS prompt screen. If your program was a straight DOS program it is likely trying to access direct and can't read FAT 32.
Only way I have seen this problem overcome, when it appears, is to reformat a drive FAT 16, load DOS 6.3, then load your application. Then load Win 98 to dual boot from a second drive. Or to redo the application in a Windows compatible language.
For best service I would retain and older PC with just DOS 6.2, the application and just sufficient other stuff to allow it to be seen by the rest of your network to transfer data back and forth.