1. Have you checked phpinfo(); that all parameters have been actually changed?
2. In addition you can try to amend time limit at runtime
if (function_exists("set_time_limit") == TRUE AND ini_get("safe_mode") == 0)
{
set_time_limit(300);
}
3. I believe having 1300 columns in table could be a sign that system design might need re factoring or optimization.