mysql/php time out issue

I'm running php 5.1.6 with mysql 5.0.45 on CentOS 5.3 box trying to loop through a while statement to send about 3000 email using phpmailer. It's worked well in the past but after an upgrade it seems to be timing out now after 200-300 emails over 1 minute or two. I've added set_time_limit(30) within the while loop to reset the time out. I've added a sleep(1) statement to throttle the program (I've tried sending with and without these additions). I've altered several config files to see if it would send to completion to no avail: mysql.connect_timeout = -1 memory_limit = 100M max_input_time = 60 max_input_time = 600 max_input_time = 0 and the following mysql config: key_buffer = 256M max_allowed_packet = 50M table_cache = 1024 sort_buffer_size = 1M read_buffer_size = 1M read_rnd_buffer_size = 4M myisam_sort_buffer_size = 64M thread_cache_size = 64 tmp_table_size = 40M join_buffer_size = 1M query_cache_limit = 12M query_cache_size= 32M query_cache_type = 1 max_connections = 60 thread_stack = 128K thread_concurrency = 4 Any where else I should be looking. Thanks!