Similar problem here. Under APM it recognizes the IP address and port number and connects as long as the USB lead is not connected between the two. It is similar with QGC with the computer recognizing the link and port with an audible comment. As soon as you attach a USB lead between the PXFmini and the PC the link goes down and both APM and QGC sit there doing nothing. QGC just says "Waiting for vehicle connection". One of the problems is that PX4 and APM use so much cpu power that it is impossible to know whether the Pi0 is just slow and doing something (due to PX4 running) or hung and not going anywhere at all (again due to PX4 grabbing al the available cycles and nothing else happening). However I would note that the green LED on the Pi0 does flash every so often which implies something is going on.
I've had the PC and Pi0 connected via usb for well over an hour and QGC continues to say "Waiting for vehicle connection". So if you cannot update the control software using a usb lead how does one do it? Now, like yourselves I cannot ssh into the Pi0 under QGC despite not having a problem previously under APM. Other than the usual Linux commands using apt-get which just contradicts APM and QGC and says the most up -to-date software is installed. Perhaps I need to setup a Linux machine to do all my drone work rather than use a windows machine which seems to go against ever producing a version of APM or QGC for windows machines.
imuguruza - is there any way one can modify the network connection to allow more than 1 machine to ssh into the Pi0? This is about the only way I can think of getting through the initial setup procedure.