After some research it appears that others have had similar issues with AJAX timeouts at ~60ms and ~120ms. Those seem like very deliberate values (like internal browser settings), and I am going to go ahead and assume from the lack of responses/solutions that we can't get around those timeouts.
Have you considered posting your AJAX request to a separate server/service which does not do any processing and can return a quick 200 OK response. Then let this second server handle the communication with the slow server. I know this sucks, but it might be your only solution (and might result in a snappier app and happier users).
Can you give any more insight into your app? Is this a PhoneGap app or is the app hosted at some domain that you can access from the browser? Are you able to provide a URL?