My guess would that your PHP code is not written correctly.

For instance, if you have a query in PHP:

$sql="select * from my_table where cid=123";

...and are using the PHP function mysql_numrows() to count the
results, and then for your next test... you're just changing the query
to:

$sql="select count(*) from my_table where cid=123"

and still using the mysql_numrows()  to get the result, that is your
error.  You'll need to use mysql_result() or some other fetch function
to get the results of the query.

That's my guess.

-Hank

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