In my view it's an accumulation of things.
e.g. I use Font agent pro. I have the same issue. When i turn off all versions of Helvetica, Helvetica Neue, Rounded etc the page renders fine. Then, when i activate just plain helvetica, problems. When i activate linotype Helvetica Neue, all is OK. All is OK when i activate linotype helvetica rounded also.
This font issue has plagued the system since the beginning of...er, OSX iirc.
I am pretty sure I hacked a solution to kill off a deeply embeded system font back in 10.6.x to stop a similar conflict. Pretty sure it was Helvetica Neue.
WHY can't apple simply attribute a seperate ID to system fonts???? This would sort it.
e.g. AppleHelveticaNeue.
I have thousands of fonts collected over years of designing. Every new system release this issue pops up over and over again.
Nightmare.