Manual update to 3.1 not working in a couple odd ways

I successfully manually updated (the automatic update always stalls) one of three WordPress installs to 3.1 but the other two will not take. I tried four times and I can still login and post but the admin still says I am running 3.0.4 and is prompting me to update again. I downloaded 3.1 twice to make sure I was installing the correct version. Also, I tried manually loading a couple more plug-ins and now they will not register in the plug-ins admin. It is as though these blogs are now running on a separate host disconnected from my ftp transfers. I checked the server PHP and mySQL versions and they are up to par.
The two stubborn sites are drpietrorotondi.org and mchuge.com.