The code that SCLogin is using to generate the registration link is almost identical to what mod_login is used. The small change shouldn't cause the Item ID to be added in one case but not the other.
JRoute::_('index.php?option=com_users&view=registration', false);
versuse
JRoute::_('index.php?option=com_users&view=registration');
Having the itemId appended to URL might come from JRoute if you're on a page with an ItemID in the URL. Are you attempting the registration button click from the same page for each of the modules?
Also could you check the 'Registration Component' and 'Custom Registration Link' settings in the SCLogin > Login View Settings tab? Do you have those set to a custom link? If so, try switching it back to Joomla.
-Melissa