The SCLogin module uses Joomla's authentication system to log the user in. The process is identical to using the mod_login from Joomla, so I don't know how there would be any difference between a user logging in with the SCLogin module vs logging in with the Joomla module.
Just to confirm, you are logging in using Joomla credentials and not a social network account, correct? The SCLogin module does support JFBConnect, our social authentication system, but I'm assuming you're not using that.
We will gladly test as well if you'd like. I'd ask you to setup the SCLogin module and Joomla login module on the same page, send us the URL and test account details (non-administrator). Then, we can login with each and wait for the timeout (just let us know how long that is) and see if the same thing happens. If so, we'll definitely be intrigued and help narrow it down.
Thanks,
Alex