I have a small AJAX enabled ASP.NET application, working fine saperately, When I
put the application inside sharepoint with all neccesary changes in the
application.master and web.config file my application is running under
sharepoint 2007, but problem is that it is not showing ModalPopupExtender in a
proper way, actually it is not picking the style sheet I have in the same aspx
page not out side the page.

I googled this issue and I found that if we change the DOCType of the HTML it
will work, I changed it and I found that AJAX running fine but the style sheet
using by sharepoint master page is disturbed. How can I solve this problem.