Hello glenster!
There are two ways:
1) do it when you create (or re-create) pop-up in FW.
Open "Set Pop-up Menu" window (click in the center of button > choose Add Pop-up Menu...). In teh righr top corner you'll see Target drop down menu. Select _blank.
2) do changes manually. But you should change not fw_menu.js but your HTML file which has pop-up menu. In the SCRIPT section on your page (should be in HEAD) you'll find function fwLoadMenus(). And do changes like shoen below:
function fwLoadMenus() {
if (window.fw_menu_0) return;
window.fw_menu_0 = new Menu("root",52,19,"Verdana, Arial, Helvetica, sans-serif",12,"#ffffff","#00538d","#00538d","#8ec6ec"

;
fw_menu_0.addMenuItem("aaa","window.open('file_path.htm', '_blank');"
;
fw_menu_0.addMenuItem("bbb","window.open('file_path.htm', '_parent');"
;
fw_menu_0.addMenuItem("ccc","window.open('file_path.htm', '_self');"
;
fw_menu_0.addMenuItem("ddd","window.open('file_path.htm', '_top');"
;
fw_menu_0.addMenuItem("eee","location='file_path.htm'");
fw_menu_0.hideOnMouseOut=true;
fw_menu_0.writeMenus();
} // fwLoadMenus()
In first 4 examples browser opens page using reserved target words, in last - just opens the page as usual (in the same window). Change it and you'll have what yuo need. I would personally choose first opportunity - rebiuld FW file and then re-export.
Good Luck!