If you're seeing the #login-modal in the URL, it likely means that the Bootstrap library isn't being properly loaded into the page. Please enable the "Include jQuery / Bootstrap" setting in the SCLogin module and that should likely fix things up for you.
I don't think your issue has anything to do with sh404SEF. If the above doesn't help, let me know a page where we can see the issue, and we'll gladly help investigate further.
Thanks,
Alex