[SalesForce] JavaScript pop up window (cross-origin frame issue)

I have button on Opportunity on click oh which i am opening a VF page window .After opening the URl becomes

https://c.cs16.salesforce.com/apex/VFpage

On Click of save button i am closing the opoup window and refreshing parent window but when i close it it show a javascript popup error after closing the window.It says

A problem with the OnClick JavaScript for this button or link was encountered:

Blocked a frame with origin "https://cs16.salesforce.com" from accessing a cross-origin frame.

I know this error is coming because the URL are different but i dont know how to solve this issue.

Can someone tell me how to solve that issue.Its urgent for me.

EDIT

Hey

I am using below code for closing the window and rereshing…

window.top.close();
     window.opener.location.href="/{!$CurrentPage.parameters.Id}";

For opening a pop window from custom button below is the code

    window.showModalDialog('https://cs16.salesforce.com/apex/PDFViewer?id={!Opportunity.Id}','',
      'dialogHeight:600px;dialogWidth:950px;center:yes;');

but when i open my pdf viewer page URL becomes

https://c.cs16.visual.force.com/apex/PDFViewer?id=006f0000004fKcj

You have any suggestions.???