I can add some extra info here which may help diagnose the issue. I don't have a github user, so I can't add this to the open bug, but please add it if you feel the info would help.
This problem seems to be timing related. If I cut and paste using the mouse a section of code from another window, (either a gedit window or another arduino ide window) the code goes in 100% correct. No problems at all.
If I type it in manually ... newlines and bad formatting happen 90% of the time (I don't type very fast, and often stop to think when I type 
).
The system I'm using for this development work is pretty chunky ... it's an 8 core Intel i7 (can't remember the processor number, but was only bought a year ago) and I have 32 Gb of ram ... way over specced for this job. But given the timing issues noted above, debug engineers may have to use a powerful system to catch the problem.
In any case I certainly see the issue on 90% of the lines that I type ... which makes beta 12 basically unusable for me 
-- Chris