Your 1.9.2 patch made a bug. I switched to 1.9.1 and the bug disappeared. For some reason, it causes pre-existing gateways when the patch is added to not appear in the starmap. Gateways in other dimensions are not affected (one in Betweenlands works fine). I have some pics with a compass and coordinates to illustrate the bug.

It likely has something to do with your fix regarding linear gateways.

Breaking and resetting the gateway does not fix the broken link.