Use your own form id for "form1", and before you say it "doesn't work" check for pop-up blockers etc.
<asp:Button ID="btnSubmit" runat="server" Text="Submit & Print" Width="150px" OnClick="btnSubmit_Click" OnClientClick="if(confirm('Do you want to submit and print the reimbursement?')){document.getElementById('form1').target='_blank'; window.setTimeout(function(){document.getElementById('form1').target=''},1000); this.style.background='#98201a url(../Images/HeaderFooterMainTemplate/loader.gif)'; this.value = 'Processing...';}else{return false;}" />