I had the same problem. When you say that you have installed all Windows Updates, have you installed IE6, service pack 1? Then I would follow that up with any critical updates having to do with security. This is on a W2K pro workstation--you did not say what OS you're using. I have NOT applied W2K, SP3--only IE updates and critical updates. The refresh problem mysteriously went away. You are also probably losing your + and - signs to the left of folders in Windows Explorer and need to restart Windows to refresh, right? After updating each time, reboot and check to see if there are any other updates to your updates. If possible, check your update installation history and see if any thing came up unsuccessful or see if you can see the installation file(s) referred to in order to make sure the install is actually there on the pc. Once you're all done, delete all temp files, scan the disk and defragment for good measure.
Please post comments with what you have found.
HTH