Yeah that is small, I think what the problem might be is that you running into the amount of queries your able to run via a single MySQL connection.
Your host should be able to increase these limits for you. Just tell them your trying to run an import script and keep getting the 'MySQL server has gone away' message.
Also if you want to try to create the package with the mysqldump option from the Settings menu in the plugin it will generate a lower query count for you...