I'm having the same problem. I have a space station with a lander that I need to refuel. I just delivered a new Roco 64 fuel tank to the station and cannot transfer any fuel out. I have cross feed enabled on all ports, and have un-docked and re-docked all of them several times. I have obey cross feed turned on, and would prefer to leave it that way, as I'm not using SSTOs of spaceplanes yet. Like Awwal, I'm running x64 Steam version on Win 10. I've tested this setup on the ground and it works fine. I don't know what else to do here.