script just starting over

Hi folks, So I have a fairly long script... I set the timeout to be longer, and timeing out has not been a problem. The script just seems to start over in the middle of itself, and then the second time it will fail for no reason I can tell. At various spots in the script I have it insert a status update to a mysql table, so I can easily track its progress while it runs. The last loop of the script is where it stops, but not at the same time each time. If that makes any sense. That's the loop that allocates new colors and sets pixels in a truecolorimage. Any ideas? -Josh