Every time I log out or shutdown Elementary OS Freya 0.3.1 after login and starting chrome 45.0.2454.85, chrome errors saying it did not shutdown correctly and I have to restore my tabs instead of them auto loading. Anyone know how to troubleshoot or resolve this issue?
Chrome/ixium always run on background by default. So, when you restart session, it try to restore old tabs.
You can try to turn off backgrounds pages and apps as described in Chrome Help.
The behavior you're seeing is probably due to this bug. As a workaround, I've been closing my browser before I log out.