mysql/php time out issue

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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!


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