Have you used the proper Win-32 APIs, or have you bodged it with hacking directly to absolute hardware addresses?

If you are hacking directly to absolute hardware addresses, then you need genuine Real-mode, single-user, single-task MS-DOS.

As Jez Smith & J. Guy have already said, Win-98 works in Protected mode; it gives the appearance of allowing you to mess directly with absolute hardware addresses, but you are actually going through the Windows multi-tasking Protection mechanisms. This is highly likely to mess-up any software which assumes that it has exclusive, direct, Real-mode access to the PC hardware.