Explorer eating up CPU Cycles

Recently I began having a strange problem. Sometimes, after logging on to my Win98SE box, the machine will appear to lock up. But it’s not really locked up because the mouse will move in very small increments. It’s clearly busy doing something.
As a test I stuck Wintop in my startup folder. The last time it did this Wintop showed it was Explorer.exe using 95%. It almost always does this for about a minute then everything is normal.
As a side note, I have a folder on my desktop with shortcuts to apps in it. Sometimes it appears that opening this folder triggers the problem because the last 3 or 4 icons don’t update like they should. They hesitate until things return to normal. But that may be a symptom and not the cause.
Any ideas?

Brian