Apparent timeout/restart of queries

I am using php and jpgaph to generate a line graph of statistics on an hourly basis from a mySQL db. I issue a query for each hour and plot the results. The problem is that, oftentimes, the queries take minutes to execute. I noticed that when the query runs for 300 seconds, but is still not complete, and another identical query is launched. I can tell by monitoring with mysqladmin's processlist command. I don't know why this should happen or how (if) I can adjust this apparent timeout. I have set the php script timeout to 900 seconds which should be enough. Where is this timeout/restart behavior initiated? Php? MySQL? Are there other parameters I can tweak so that the query can finish and not be re-issued? One other data point. Even after killing the browser process, the php/mysql conncetion seems to live on. If I use mysqladmin to kill the query the query for the next hour is then launched, so the PHP script is clearly still running.