I just upgraded from 4.5 to 4.6 and installed Organic Groups. Weblinks stopped working at that point too, and so I upgraded to CVS version - as was described in another forum topic and seemed to work for others. However, now when I go to http://activeresponse.org/weblink or http://www.activeresponse.org/og I recieve a 403 - Page Not Found message. I found that they are bouncing me to the subdomain activeresponse.classstudio.com.
So far I have found two modules with changed database tables.
The private message module has added a column called "newmsg" (if my memory serves me correctly), the mysql error said it could not find this column.
I manually added the column
The webform module has renamed the confirm column to confirmation. I manually edited the name.