In the SP game (haven't tried MP yet so I don't know if it's a problem there too), there is a jump hole between Leeds and Cambridge, but when you first use it during the storyline, going from Cambridge to Leeds, it doesn't show up on your Leeds system map. It's possible to fly around and find it and use it to go from Leeds->Cambridge, but it still isn't tagged on your map.

I wondered why this was so, and I looked at the ini files for both systems, and I couldn't see any reason why - the definitions of the jump hole looked perfect like all the others. (Which makes sense, considering they didn't send you to the center of the sun or just wind on endlessly.) I gave up on fixing it through the ini and just decided to make my own Leeds-Cambridge hole to replace the 'broken' one. First I tested making a hole from Leeds to Sigma-11 just to be sure I had the hole syntax correct. When that worked, I changed the hole to go from Cambridge to Leeds. When I entered the game to test it in the Leeds system, I tried to dock on the TEST_REPLACE hole, and instead my ship flew to the location of the original Leeds->Cambridge hole. Even better, the 'missing' hole now showed up on my map! I saved the game and went back and commented out the TEST_REPLACE hole in Leeds (but not Cambridge), and the original hole was still marked on my map. Then I commented out TEST_REPLACE in Cambridge, and everything was still fine with the original hole - marked and usable in both systems.

So. I don't know that this has shed any light on why the hole wasn't getting marked in the first place. But maybe if someone ends up having similar problems with new jump holes or holes in new systems they create for their mod, this would give them an idea of how to fix it....