Several people have reported similar issues (
Controller Doesn't Reconnect), especially with wireless connections going into standby mode, etc.
Initially I was unable to reproduce the problem with a Steam controller or wired Xbox 360 controller, but another person reported that holding Y and hitting the Steam button would cause this (to turn it off immediately, rather than just holding the Steam button for a couple seconds), which I could reproduce. While testing that time, I also reproduced it once by running the battery down, which I hadn't tried before (and didn't deliberately do that time; it just hadn't been plugged in for some time).
Can you connect the controller directly to your computer? If so (a quick online search didn't turn up an answer), do you have the same problem there?
