This is one of the most annoying bugs/non-features in the entire program. In 11 it is improved, since the transparency setting is the section/elevation itself, but that doesn't help you much at the moment.
I had to do some experimenting in 10 to refresh my memory about what is happening and it appears to be a bug. As you know elevation transparency is controlled by the 'Transparency in Shading' switch in the 3D window settings dialog. Real intuitive. From what I can tell the setting is working in the window itself. I can activate a view and the glass is opaque, then I can turn on transparency and it becomes clear, then it's opaque again if I reactivate the view.
The drawing, however, is hosed. The view comes in correctly, but if that 3D window transparency setting is switched on, and the drawing is updated, the glass in the drawing goes clear. Turn transparency off and update the drawing, still clear.
Of course there's no 'Redefine View' for non-3D views, so that's out.
You have to replace the drawing, but then that drawing is no less vulnerable to the switch.
Also, the drawing will use the state of the switch at the time the drawing is placed, so make sure it's off at that moment.
It's made worse by the fact that the transparency switch setting is saved with 3D views, so if you activate a 3D view that has the switch on, you can easily turn it on without realizing it.
And while you can redefine 3D views, there's no feedback on the state of the various options as you perform that redefine.
You basically have to swear to always make sure that switch is off before updating your drawings. You weren't busy thinking about anything else at that time were you?
So it's bad design (a 3D setting affecting a 2D view) + a serious bug (views and drawings not acting the same) + poor feedback (can't redefine 2D view, can't tell what's being redefined with a 3D view) + direct impact on output (ugly, wrong elevations) = software malpractice.
Sounds like a prime candidate for a critical fix, but alas it's in the previous version so don't hold your breath.
HTH, as if.