It sounds like you have a few things going on:
First, the problem updating the folders. There's an issue where you can make a new catalog and import images. But after you save and close it, you can't add more images after you reopen the catalog. We have a service pack coming out soon, and that issue is fixed in it. However, there's a workaround you can implement now. If you change the volume label on the drive where the images are stored, the problem should be fixed.
Peter is right about the temporary files - If you kill Media rather than closing it normally, the temp files left on the system fool it into thinking someone has the catalog open already. See article http://support.microsoft.com/kb/953109
for full instructions on deleting the temp file.
The icon getting "stuck" is an issue that we fixed in Service Pack 1, or thought we did, but there have been a few isolated reports of this happening to machines with SP1 installed. However, that does not mean that the process didn't finish. Import or update generally finishes fine. The icon just keeps going around.
Just as an aside, if you drag an image from one folder to another inside Expression Media, or use the Transfer to Folder feature, the file counts in the folders update automatically. The only time you need to update folders in the Organize Panel is when you have moved files around in Windows Explorer.
Hope this helps,
Hope this helps.