includes/classes/shipping.php makes it so the "cheapest" shipping method available is selected. So if USPS is less $$ than the other, this is why :)
Line 114-ish
function cheapest() {
if (is_array($this->modules)) {
$rates = array();
reset($this->modules);
while (list(, $value) = each($this->modules)) {
$class = substr($value, 0, strrpos($value, '.'));
if ($GLOBALS[$class]->enabled) {
$quotes = $GLOBALS[$class]->quotes;
for ($i=0, $n=sizeof($quotes['methods']); $i<$n; $i++) {
if (isset($quotes['methods'][$i]['cost']) && tep_not_null($quotes['methods'][$i]['cost'])) {
$rates[] = array('id' => $quotes['id'] . '_' . $quotes['methods'][$i]['id'],
'title' => $quotes['module'] . ' (' . $quotes['methods'][$i]['title'] . ')',
'cost' => $quotes['methods'][$i]['cost']);
}
}
}
}
$cheapest = false;
for ($i=0, $n=sizeof($rates); $i<$n; $i++) {
if (is_array($cheapest)) {
if ($rates[$i]['cost'] < $cheapest['cost']) {
$cheapest = $rates[$i];
}
} else {
$cheapest = $rates[$i];
}
}
return $cheapest;
Edit for file reference & Store pickup vs USPS