10.4.5 I believe is when they added more "lookup in progress" functionality to block the submit button and such while a lookup is in progress to prevent issues submitting with incomplete data.

As a result, the lookup events are now interacting with the action buttons, so if you alter them in significant ways it can break those events and cause it to not remove the "retrieving field values" message, or possibly even prevent submission of the form.

If you want to have your submit button in a different location, rather than moving the existing one I would suggest hiding (not removing) the built-in one, adding your own, and adding an event handler that triggers the click event on the default button(s).

For example,

CSS

.Submit {
    display:none !important;
}

JavaScript

$(document).ready(function(){
    $('#customSubmit').on('click',function(){
        $('.Submit').click();
    });
});