Okay, let's go through the fields that need checking for a hypergate to work
General: type 1
"Landing" => "Allow player to land/dock", "Planet is inhabited", "Planet is a space station"
The minimum landing status is yours to choose. The hypergates for which one needs Sigma Shipyards' codes have their status set at "32767", so that no one except those with the "Hypergate Access" ränk can have access to the hypergate system.
"Defence" => "Fires only when provoked"
"Animation" => "Live"
"Misc." => "Hypergate", Transition frame: "37"
Once you have made sure all these fields are checked (and those are all the fields and the only fields that should be checked, I think) in all the spöb resources that are meant to be hypergates, you go in "Misc." and link them up between each other. Make sure every link is mentioned in each spöb resource it concerns.
If you still don't manage, and if no one thinks of other things you need to do, then it might be easier to post your plug.