System Information
Linux bubastis 3.10.25-gentoo #10 SMP Thu Jan 30 22:17:35 UTC 2014 x86_64 Intel(R) Core(TM) i7-4800MQ CPU @ 2.70GHz GenuineIntel GNU/Linux
01:00.0 VGA compatible controller: NVIDIA Corporation GK107GLM [Quadro K1100M] (rev a1) (prog-if 00 [VGA controller])

Blender Version
Broken: git 2c69f1e574587c2364e9a94b45d0b363ffeebf61 and probably earlier

Short description of error

When grouping a set of VSE strips into a meta strip sometimes the translucency is broken.

Exact steps for others to reproduce the error

When grouping a set of VSE strips into a meta strip sometimes the translucency is broken.

In the VSE
Add a color strip on the bottom (1)
add a strip over that (2: from scene or image sequence).
Add another strip over that (3) from a scene that has transparency (its sky is unchecked in the Render Layers).
Set both strips to blend = Over Drop or Alpha Over
Animate the opacity on the top strip to make it fade out over time (from 75,1 to 90,0
Animate the opacity on the middle strip (2) to make it fade from 60,0 to 90,1 (fading in).

Render images at 60, 67, 75, 82, and 90.

Now group the top strips (2,3) to make a meta strip. Since the meta strip defaults to Replace (which seems like a bad default to me) adjust it to Over Drop or Alpha Over

Render images at 60, 67, 75, 82, and 90.

Become disappointed.