Versions:
jquery 1.8.3 (tried with both local and from google cdn)
.net 3.5 (c#) (Visual Studio 2015 Community Edition)
chrome Version 56.0.2924.87 (64-bit)

Using a .html file the dialog works perfectly, however if I use an aspx file with or without master page the dialog always positions vertically centered and horizontally to the left as per attached screenshots. I have tried this on a blank project as well as an existing project that I am supporting. Screenshots attached at bottom.

Javascript used is:

function testAlert() {
$.alert({
title: 'Alert!',
content: 'Simple alert!',
boxWidth: '30%',
theme: 'material',
useBootstrap: false,
});
return false;
}

function testConfirm() {
$.confirm({
title: 'Confirm!',
content: 'Simple confirm!',
boxWidth: '30%',
theme: 'material',
buttons: {
confirm: function () {
$.alert('Confirmed!');
},
cancel: function () {
$.alert('Canceled!');
},
somethingElse: {
text: 'Something else',
btnClass: 'btn-blue',
keys: ['enter', 'shift'],
action: function () {
$.alert('Something else?');
}
}
},
useBootstrap: false
});
return false;
}

Basic alert:

Modal: