Can you post your revised code? Are you re-using the statement handle? What's the error in the error_log (or if you run on command line)?
Also, try adding
$|=1; in your script to make sure it's not buffereing so yuo'll see output as it's happening.
If the loop to execute the queries is good now (resuing handles, etc), then this probably just goes back to the issue mentioned elsewhere in this thread about SQL performance .. the speed will depend entirely on your SQL, table schema, and indexes (can you provide any of those?).
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