StZ

http://nos.nl/video/714736-gratis-internet-is-schatkamer-voor-hackers.html

Windows automaticly assumes it's the only operating system, thus replacing your bootloader. What you'll need to do is reinstall grub using a live cd. https://help.ubuntu.com/community/RecoveringUbuntuAfterInstallingWindows

I always recommend new android people to run stock for a couple of weeks, before flashing to a custom rom. That way, the rom flash will be magical, instead of 'meh'.

Over at DuckToolkit there are some options for creating new user accounts with administrative privileges. Not sure if that's what you're looking for since you need command prompt access. For targeting multiple OS's, you obviously can't use the windows payload. I remember seeing a custom firmware somewhere that would excute different payloads based on capslock, numlock or scrolllock beeing turned on. Perhaps that helps.

I noticed the same issues a couple of days ago. At home it works fine, but at a mate's house, with only a wireless N router, it wouldn't connect at all.