The first time I rooted I had a similar problem. Even after flashing super-user Titanium would tell me I wasn't rooted.
In the end downloading a different super user version fixed the problem.
Not sure what to suggest for your usb problem tho...
XDA Developers was founded by developers, for developers. It is now a valuable resource for people who want to make the most of their mobile devices, from customizing the look and feel to adding new functionality. Are you a developer? | Terms of Service