I saw this in XP Annoyances while looking for something else, and I thought it a good checklist for you:
Clear the documents menu
Clear Unwanted Entries from the Start Menu's Run Command
Check for any viruses on your system (some users have reported the NEUVILLE virus)
Search your hard disk for all .PIF that point to programs on a floppy drive
Take out LocalLoadHigh=1 from your MSDOS.SYS file
Check HKEY_CLASSES_ROOT/CLSID in the Registry for any references to OCX's or DLL's referenced on the floppy.
Double-click on the System icon in Control panel, choose the Device Manager tab, and delete the GENERIC FLOPPY DISK entry (found under Disk drives). When Windows restarts, it'll re-detect the drive and the problem should go away.
Other programs known to cause this problem:
Norton Navigator - Clear Norton Navigator's Run history (or disable the Run history all together), and download the bug fix from Symantec
McAfee Antivirus '95 - try removing this program entirely, or just disabling the Access & Shutdown options in the Scan Disks On area in the Detection tab of the VShield Configuration Manager.
FirstAid '95 - try removing this program or disabling certain features.
Long Filenames for Windows 98 - View Software has a patch that supposedly fixes this problem.
HiJack for Windows 98 - turning off "Enable HiJack shell extensions" in the HiJack Control Panel.
Konica Picture Show - try removing this program entirely.
Norton Antivirus 2000 - turn off the options that scan the floppy drive during startup and shutdown
Hope it gives you some practical clues.
Best.
Bill