For details on setting up your own custom theme for the SCLogin module, see the link below:
www.sourcecoast.com/sclogin/documentation/themes
As for the issue, it seems that JSM2WIN is altering the JPATH_ROOT or JPATH_SITE variables which the SCLogin module uses to create the CSS link. You can try the following, but I don't know if it will work.
* Edit the /modules/mod_sclogin/helper.php file.
* Around line 59, you'll see the following block:
$paths[] = JPATH_ROOT . '/templates/' . JFactory::getApplication()->getTemplate() . '/html/mod_sclogin/themes/';
$paths[] = JPATH_ROOT . '/media/sourcecoast/themes/sclogin/';
$theme = $this->params->get('theme', 'default.css');
$file = JPath::find($paths, $theme);
$file = str_replace(JPATH_SITE, '', $file);
In there are 2 instances of JPATH_ROOT and 1 of JPATH_SITE. Try updating them so they are all the same (JPATH_ROOT or JPATH_SITE). Then, test if it works. If not, try the other way.
Let us know if having them all with the same value fixes things for you. Otherwise, you may need to contact the JSM2WIN devs to help us understand why those variables aren't the same any more.
Thanks,
Alex