I can reproduce it in 5.3.3.
Seems like it happens with numeric indexes only:

//create object
$obj->q = 'something';

//convert object to array
$arr = (array)$obj;

//modify element
$arr['q'] = 'something else';

//dump final array
print_r($arr);

Result:
Array
(
    [q] => something else
)


This way works:

//create object
$obj = new stdClass(array(
	1 => 'something' 
));

//convert object to array
$arr = (array) $obj;

//modify element
$arr[1] = 'something else';

//dump final array
print_r($arr);

Results:
Array
(
    [1] => something else
)

@felipecg00:
1) yes, this happens only with numeric indexes
2) in your second snippet you are creating an empty 
object and then assigning new element instead of modifying existing one. Dump your 
initial object in the beginning to see what I mean.

You are right! Don't know why I thought that would work. Guess I need to sleep a bit.

This is documented behaviour, and a duplicate of bug #45959 -- in essence, it's a known issue, but not one that's likely to be fixed for performance reasons.