When you are plugged into the computer via the usb, the Reader cannot be used in any way expect to transfer ebook to and from the device.
Initially I would say some of the problems may be due to not charging fully but I would wait until the Reader has been fully charged via wall plug before trying to troubleshoot. If you battery was completely dead it may take an overnight charge to get it in working condition.
If all else fails, attempt a hard reset as this helps with fixing some stubborn problems. Do a search for 'Sony Reader Troubleshooting Guide' for the steps needed to perform a hard reset.
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