I did find a little info last night before heading in to work.
I was searching the Microsoft Knowledge Base and found an article on "EMachines/Win98SE".It was about using the Recovery CD that came with the EMachine.It caused BEEPS at shut down and something else,I'll see if I can find it again today sometime.Anyway it said to apply the "MSPatch",like I said I'll see if I can find it.
At the time it didn't read like your prob but the more I thought about,it just might be.
All it said was that using the Recov CD caused some files to not load properly,causing problems at Shutdown.BEEPS at Shutdown and restarting...
You never mentioned re-starting so I never bookmarked it...

sry.
I'll find it for you,unless someone knows of this bug??
Cactus