<< Odd problem. Also made me wonder why you were trying to shut down Seti, but I suppose as the owner of the PC you at least ought to have the ability to shutdown Seti, but I really think someone is trying to tell you something.....
None of the following suggestions may help, but they won't hurt. Seti sometimes has a problem shutting down when you try to shut down Win98 )hasn't been a problem for me on W2K or XP). Going into the windows/system file, and unchecking the "warn if still active" box in conagent.exe fixes the shutdown problem. I'm assuming the Prioirty is set to Low? Last thing I'd try is a reinstall of Seti Driver/CLI, perhaps one of the files in the CLI or Seti Driver got fubar'ed somehow.
Edit: <<And that is not even counting all the trouble it is to download 1MB+ WUs every few hours(I have a 1600+).>>
Got a fix for ya', run SetiQ, set it to connect at 3:00 AM, you'll never even know it happened. 😀 >>
I did that "warn if still active thing" When i first installed the drivers.......yeah, i don't know why i want to shut down SETI no need, but as the ruler of my kingdom(my desk) i think i should have full control over what goes on, and i think the fact that i'm not in control here is annoying me heh.....oh well, i geuss i'll just leave it running....i'll reinstall as soon as the race is over so in case i screw something up i won't loose time