I have looked to see if thsi is a known issue or not, and have found no other mention of it, although a similar issue is reported involving layer transformations...

Given two layers:
A (Mode Normal, Opacity 50), and
B (Mode Normal, Opacity 50);

When:
Layer A is selected and via the right click menu  in the layer dialogue, instructed to 'merge down', the reslutant layer B has Mode Normal, Opacity 100.

Objects previously drawn on layer B still reflect the previous Opacaity, and adjusting the Layer's opacity back to 50 further fades the existing items.

New objects follow the opacity 100 value, and fade correctly if the layer's opacity is altered.

From the Gimp Help FIle

"7.7. Merge Down

The Merge Down command merges the active layer with the layer just below it in the stack, taking into account the various properties of the active layer, such as its opacity and layer mode. The resulting merged layer will be in Normal mode, and will inherit the opacity of the layer below. If the layer below is not opaque, or if it is in some mode other than Normal, then this command will generally change the appearance of the image.

The most common use of Merge Down is to construct a layer, by starting with a “base layer” (usually opaque and in Normal mode, so that you can see what you are doing), and adding a “modification layer” on top of it, with whatever shape, opacity, and layer mode you need. In this case, merging down the modification layer will combine the two layers into one, without changing the way the image looks."

Unless I am missing something, current function is opposite of intention.  Lower layer is reset instead of being honored.

Ubuntu 12.04 64 bit
I-7 Processor
8 GB ram
Gimp 2.8.8 (from Ubuntu Repos)