I had the same problem with my medians, and have figured out a fix for this!!
After 2 days of reworking corridors, rebuilding assemblies, and beating my head against the wall, I decided to start playing with some of the features in the corridor properties that I have never touched before. Come to find out, the fix to this is to change ONE setting and it fixes the whole corridor. See below...
Once I changed this from Inward to Outward, and rebuilt the corridor, it worked like a charm.
This has been logged as a defect by Autodesk. See the link below.
I tried your Branching setting suggestion, and I still get incorrect Corridor and Corridor Section construction when crossing the Centerline. See the image below.
Ah, crossing the alignment, totally different ballgame!
yeah although branching does fix the whole feature line cutting the wrong way thing.. it still leaves a hole in the featureline where it crosses the centre line..
MY solution is rather simple. develop your corridor off a different centre line. Its kind of annoying as it plays with you chainages but still it works.