Hey there dineshM,
How are you doing today?
Some shortcodes (including the contact-form-7 shortcode) will only work when loading method is set to "Page Footer" and "Custom Ajax".
Could you please try using either the "Page Footer" or "Custom Ajax" loading methods, you'll find the option in Popup -> Settings -> Popup Loading Method, see screenshot http://screencast.com/t/RtSWp6aLL.
Hope this helps :)
Best regards,
Bojan