Trouble connecting after upgrading database

I run a webserver for several users and one of them uses WP. I have moved our existing webserver to a new machine. The only machine had a MySQL 3 database. The new server has a MySQL 5 database. All the data in the tables has been transferred to the new databases. However, all I’m getting when I try to load the user’s page is a bunch of errors that the connection was lost during query. I have tried connecting through the command line to mysql and and can run the queries. Can anyone tell me what the problem might be?