I played through Space Shuttle Project not too long ago. The game is playable from start to finish, as none of the gameplay screens are affected by this display problem.
There seems to be only a handful of screens throughout the game that have this issue. The title screen, the pre-launch cockpit screen, and some (but not all) of the post-mission screens, like the newspaper if I recall correctly.
I found this old forum post that looks like it might explain the issue. Maybe someone will understand the technical part better than I can.
http://forums.nesdev.com/viewtopic.php?t=4243#p35209Part way down the screen its switching which pattern table is used for the background. Those emulators aren't getting that switch so the bottom half is using the same tile set as the top half. Its doing that on scanline ~119 (likely sprite 0 hit) by changing the $C000 MMC1 register to select a 4KB chr bank at $1000.
Hope this helps.
