This is because
foreach ($conditions as $condition) {
$queryData['conditions'][] = $condition;
}
loop ignores keys (it uses ‘[]‘ to assign elements).

If you change it to something like:
foreach ($conditions as $key => $condition) {
if (is_string($key)) {
$queryData['conditions'][$key] = $condition;
} else {
$queryData['conditions'][] = $condition;
}
}
it will work properly for both cases (with and without array key).
I use this improved version of your code in one of my projects and it works very nicely (keyd conditions are IMO nicer to use and more standard for Cake 1.2 than plain string ones).