It's quite a mystery. I had a worse problem a couple months ago with SpyAxe, one of the most vicious malwares I've ever encountered. Took me a week of research and fighting to kill it, eventually going to safe mode and manually extracting files to desktop and then death in recycle bin.
The problem affects all users of this computer and there is no indication of WHY explorer persists in taking up 99% of the cpu except when grudgingly yielding slightly to other programs.
I at first suspected malware because explorer goes ape only when the internet cable is connected. If I start the computer without the cable connection, explorer quickly goes to idle as it should after startup.
That sure looks like an internet attack, but at this point I'm guessing it's a separate Windows problem, although always triggered through the cable connection when turned on.
I have a physical firewall via a wireless network, the XP firewall, and McAfee virus protection through AOL. I run AdWare and Spybot periodically, and just installed Spyware Doctor which seems exceptionally efficient.
But none of these have ever solved the explorer.exe slowdown. The only relief I've had is through manually messing with it. I've again gone into safe mode and examined the entire file setup by function and date and find nothing suspicious.
Internet searches show explorer.exe slowdown to be a long and enduring XP problem that apparently has nothing to do with any virus, spyware, or malware. I "fixed" it first time by refining cable connection, but it was back the next day. I looked for a reported leak when running mopic but no joy.
One side benefit is I've really scrubbed my computer settings and have them optimized as far as I can tell. With explorer.exe tamed, the computer seems to run fast as new.
Thank heaven this weird practice of disabling explorer.exe after startup and then running it again keeps my computer running smooth all day.
I'd still like a permanent fix, but it may come eventually from another XP update sometime in the future.
Meanwhile, if you hear of any fix for this problem, please let me know.