Here is my view, based on my own pain.... The IBM with Windows 98 probably has a "real" serial port. Does your laptop have a USB-Serial adapter perchance? low-cost USB-Serial Adapters have occasional issues depending on how touchy the piece of equipment is.
So I bought a high-priced USB-Serial adapter. But when I plug it in, Windows XP assigns it as COM6 and my software only goes up to COM4. The trackpad on the laptop hogs one of the COM port addresses, and the laptop hogs the other. In most cases if you have something on COM1/COM2 there are usually issues with anything you try to do on COM3/COM4 so that kind of bites - I have to switch the modem to COM6 when I want to use the serial port with the older software, and my Hicom 150 STILL won't work using a USB-Serial adapter no matter what I do, so I have an old Win98 laptop laying around just for that one switch.
Anyway... If you have a "real" com port most of this probably doesn't apply, but still look for COM port conflicts in Windows.