Amol,
If possible why don't you create a user control instead of the popup. And show the control using styles (position:absolute) to float the control and on the click event of the grid set the original page textbox, using the code like -
((TextBox)Page.FindControl("textbox1")).Text = "your value";
And also if you don't want the control, and want to use the window. There may be issue with the window instance name, change the window instance name each time you open a new window. Like manipulate and use different value for 'winname' in
winname = "win"+<some unique of your own logic>;
window.open(url,winname);
And use the opener.document.getElementById() method in the child window to set the parent window fields.