No, the problem is not due to your file system, but a compatibility issue with the software. Microsoft has issued a statement about the problem, and it appears that there will be no update.
"<font color=red>This section applies to you if you own one of the following SideWinder game port devices:
SideWinder Force Feedback Pro
SideWinder Precision Pro
SideWinder Force Feedback Wheel (game port version only) SideWinder Game Pad
SideWinder 3D Pro
The SideWinder software (version 3.02) included with these SideWinder game port devices is designed to work with Microsoft Windows 95 or Windows 98. If you have Windows 2000 or Windows XP, the operating system includes device drivers for these game controllers listed above, so the device will function properly on both Windows 2000 and Windows XP. However, the accompanying SideWinder software (version 3.02 or any previous version) will not function, so you will not be able to create profiles for these devices using the SideWinder software on Windows 2000 or Windows XP. Microsoft is not planning to update the SideWinder software (version 3.02) for game port devices."</font color=red>
<A HREF="http://www.microsoft.com/hardware/sidewinder/SWUpdate/default.asp" target="_new">SideWinder Support</A>
Toejam31
<font color=red>My Rig:</font color=red> <A HREF="http://www.anandtech.com/mysystemrig.html?rigid=6847" target="_new"><font color=green>Toejam31's Tantalizing Tantric Toy</font color=green></A>
<font color=red>Second Rig:</font color=red> <A HREF="http://www.anandtech.com/mysystemrig.html?rigid=15942" target="_new"><font color=green>Toey's Dynamite DDR Duron</font color=green></A>
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<font color=purple>"Procrastination on your part does not constitute an emergency on my part."</font color=purple>