With multiple strokes I notice two issues which affect the stroke visibility in a way which seems to crop from the stroke either its outer or its inner part.
One issue occurs when a layer opacity is set from 100 to 99 %: that makes the outer stroke part disappear at once, whereas a reduction of opacity isn't visible for the rest.
The other issue occurs if the fill color of the group layer gets ticked to invisible in the appearance panel: that makes the inner part of the stroke partially disappear.
multistroke grouped issues.m4v
I don't know if it is related to the recently reported and known crash issue of the thread linked below. Although it is shown with the same Test.afdesign the issue shows something very different. I have not tested whether it influences an export, I just got confused by the appearance.