PHP Page to Load XML page into MYSql fails on new SQL server, needs a little cleanup(repost)

I have a really simple PHP script which loads an XML file and then writes it to a mysql database. It uses mysqli_multi_query($dbh, $statement). Script works fine on my one mysql server. I am looking to port this to a new machine that has a new mysql install. When running this script under this new mysql 5.1 it hangs. The old server was 5.0. I am not sure if that is my problem. I get the error on the new server, 'mysql server has moved away' and the log file in the new mysql server fills up to 170+ megs I messed around with all the buffer sizes and even took the [login to view URL] from the original mysql server. php file is attached. I am thinking the solution is to modify this code so that it batches the inserts rather then trying to insert all 5000 lines in one shot. If needed I can attach the [login to view URL] if somone thinks it is a mysql config issue but i did use winmerge to check the version on the old and new servers and it was almost exactly the same