Please help with an odd problem

As some of you know I recently launched an iPhone application. Part of that application allows for updates to be displayed as a small icon over the large icon launches the application. This is very common among news applications.

To make this work there's a whole lot of internal communication that needs to happen with our website and some other services. I'm happy to report that all of it works, kinda.

Here is the problem that I'm experiencing and it is cron related.

The way it works is very simple. In our system when an article is published I increment a table where we store all of the iPhone IDs.

+----+----------------------------------+---------------+
| id | device_id | article_count |
+----+----------------------------------+---------------+
| 4 | D9E5C452018AA5B7781BDB185D03XXXX | 0 |

I then made a cron hook...

/**
*A cron hook function to run the iphone article count update whenever cron runs
*/
function gpiphone_cron(){
gpiphone_pushBatchNotification();
}

... that runs a simple function to package up all of the iPhone devices with a count greater than zero and send that off to urban airship that does the actual push to the device and then resets the count in the table to zero.

...

/**
* This function pushes the json dictionary to urban airship for processing
* @param dictionary $json A Jason dictionary containing the device aliases and batch and/or message
* The required format appears below
*/
function gpiphone_pushBatchNotification(){

$json = gpiphone_batchJsonArticleCount();
do_post_request("https://go.urbanairship.com/api/push/batch/", $json);
db_query('UPDATE {iphone_pushregistration} SET article_count = %d', 0);

}

/**
* This function compiles a Jason feed for batch processing all of our article updates
* While it takes no arguments it is important to note that we are using device aliases not device tokens to communicate with urban airship
* [{"aliases": [ "D9E5C452018AA5B7781BDB185D03XXXX" ],"aps": { "badge": 1 } },{"aliases": [ "1B789D6D89F0FE1D45B231CE2DCFXXXX" ],"aps": { "badge": 1 } }]
* @return json $json
*/
function gpiphone_batchJsonArticleCount(){

$json = "[";
$sql= "SELECT * FROM {iphone_pushregistration} WHERE article_count > 0 ";

$result = db_query(db_rewrite_sql($sql));

$rows = db_affected_rows($result);
$i = 1;
while($data = db_fetch_object($result)){
  $json .='{"aliases": [ "'.$data->device_id.'" ],"aps": { "badge": '.$data->article_count.' } }';
    if($i < $rows) {
      $json .= ",";
    }
    $i++;
    }
$json .= "]";
return $json;

}

The key problem is that it works, if I run Cron manually. However if I just let Cron do its thing I see that the the table is empty and set to zero but the iPhone is never getting updated with an article count.

So the question is why is Cron running differently when I run it manually then when it runs on its own? I do know that it's running on its own because it's performing a large number of other functions.

Please help me. Is there something that Cron does differently when it is run manually? Can you give me suggestions on how you might triage this problem. I'm really at a loss because everything is working.

I've never really needed to hook cron before and so I'm just not sure if I'm doing it correctly, any help is greatly appreciated.

Greg