First off, your ship wobbles slightly when you rotate it, and that makes the screen scroll very slightly. The hotspot on your ship is off center, if you center it it won't wobble any more.
Second, your Tiled Background textures aren't a power of 2 square. You should go for a texture that's 128x128, 256x256, 512x512, etc. Since they're not sized properly they don't tile properly when the screen scrolls, as it does ever so slightly because your ship wobbles.
Fix those two things and the flickering will stop. Well... okay, it didn't completely stop 100% for me, but it helped quite a lot. There's still a little hint of a flicker every now and then, but it's not bad, and hardly noticeable unless you're looking for it. Ashley has said there's still work to be done on the Tiled BG so maybe that will help.
Or you could set your filtering to Point and it goes away completely. Since you have such a hi-res game it still looks good with point filtering, imo.