I've put many, many hours into this game, and this issue has just started...when I log out of my game and log back in, all my waypoints are gone.

For example, I found the location of a crashed ship, and the icon was on the screen and in the compass-thing at the top. I logged out, and the next day when I returned it was gone. Once, they even all disappeared while I was playing! I'm positive that they persisted previously whenever I logged out and back in.

Anybody else have this problem?

OK...my waypoint issue seems to be fixed, except now it is automatically tagging everything with custom waypoints! As I fly along, the little white circle/dot thing is tagging almost all structures, save points, damaged machinery, etc.! What the heck...

It's a known issue and I'm experiencing it since the beginning.
I'm still waiting for a fix. Maybe on next patch.
We'll see.