I found the same issue with my w98 ie6sp1.
In my case I found this problem occured if I accessed the java control panel.
If I did NOT access the jcp then the machine would shutdown proper.
Accessing the jcp does not show up as a task but it does show up as a process.
That process seems to be what shutdown was having a problem with.
I tried a reload of java (great fun on d/u) no help.
I tried a process killer....no help
I then found that java sites did not display proper. (slightly fuzzy)
Bottom line the product went to the S-can.
After I installed this to use in place of Microsoft VM I have experienced shut down problems with my "Windows 98SE".It reaches the "windows is shutting down" screen and freezes.I did not have any prior shut down problems before installing the Sun Java. My browser is IE6.0SP1