Hi,
If you enable the account activation, after registration "Joomla" will send an email to user to let them activate their account by themselves. But this handles by Joomla. Not by Virtuemart, not by our Template. This is Joomla's duty.
You may try this:
Open your FTP and find this folder:
/templates/flexible_lightmart/com_users/
and rename it to this:
/templates/flexible_lightmart/com_users2/
By this folder change, you are actually disabling the LightMart's template overriding on com_users pages. So the official Joomla com_users layouts will be used. Try this folder renaming and see if disabling template overriding fixes the account activation problem.
Regards,
Support & Development