You can use JS event on open lightbox:

var Ajax = require('elgg/Ajax');

var ajax = new Ajax();

$(document).on('cbox_open', function() {
    $.ajax({
       url: elgg.get_simplecache_url('my_plugin/my_plugin_js.js'),
       dataType: 'script'
    });
}

Your general problem is code in a module executes once. It sounds like your module should add an event listener for when colorbox opens. Just curious, what does that code do?

@Steve Clay: the code generates a paypal button. So it may have different values, e.g. cost on each popup open.

But the JS is not loaded after 1st popup, even if it has a simple command such as "console.log".