Hyper-V VMs that are turned on are missing in Hyper-V Manager

The main issue you have is that Hyper-V manager on Windows 7 And Windows Server 2008 R2 cannot manage Hyper-V on Windows Server 2012. You need to use Hyper-V Manager from Windows Server 2012 or Windows 8.

You probably haven't configured WMI and DCOM for remoting on your client and server. John Howard wrote a series of blog articles explaining how to connect to a non-AD integrated hyper-V server remotely and several of these steps apply to doing the same in hyper-V as well.

The simplest way to do that is to download the Hyper-V remote management configuration utility script from MSDN's code sample site and follow the instructions on John's blog.