New approach!
Instead the previous one, that redefined the slider each time the popup is opened (causing other problems), I have initialize the slider directly in the User Web Control
:
<script type="text/javascript">
var slider;
$(document).ready(function () {
slider = $('.bxslider').bxSlider();
</script>
And then the control that launchs the popup stand as:
<asp:Button id="Button1" runat="server" OnClientClick="$find('PopupBehaivourID').show(); slider.reloadSlider(); return false;" Text="Show me!" />
ie, I'm now using a method that reload the gallery each time.