Did you turn the Popup back on, and can you see the verses popup using the Macro hotkey? Also, have you tried the Bible popup hotkey? Hotkey is installed with a few versions, but you can download and updated index file that works with e-Sword. From the main Hotkey window, click the HotKeys menu, click the Select Version, and select the last option, "Download Lastest Index File" which will give you access to more versions if you have them in e-Sword. The Macro function give access to all the versions in e-Sword, but Popup does not. The reason for the Bible popup is that with the most recent versions of e-Sword, the macro functions are at least an order of magnitude slower that they used to be.
Try both the Macro and Bible popups, with the Macro popup enabled to confirm capture. And if that does not work, where are you located, perhaps we can skype or talk on the phone sometime.