This is expected for the following reasons:
-If every 1 px line is not falling EXACTLY on a comp pixel, subpixel sampling will make it disappear in places.
-If your layer is scaled down at any stage, or if you are exporting at half quality instead of full, it stands to reason that a 1px line will disappear in places.
-jpeg is a lossy format, which means some information is dropped at export
I would recommend using a slightly thicker line.