The file below illustrates the problem.
Create a copper area on top and bottom of board. Create some vias in between. Mask the top and bottom solder mask (with a rectangle) as you would if you wanted bare copper to solder a mosfet to for thermal reasons. Render the photo or gerber. The bottom surface correctly renders. The top does not. The vias are not visible.
https://drive.google.com/open?id=1c2K32OgADLJ835bzxWHK_RrQzdrTMS1Q
Certainly there is a rendering problem with the photoview and the JLCPCB viewer but if you download and check the Gerbers using gerbv then they are correct.
Get gerbv:
http://gerbv.geda-project.org/
(There is a port of gerbv for Windows on the sourceforge page.)