Confirmed this behavior as of 26/01/2014.
Applied black pain on mosin on the 3rd floor of an industry building. The mosin disappeared. The mosin had the compressor, PU scope, and bayonet. It was later located 10-15 meters north of my location but was floating in the air. Had to stand directly under it to retrieve the rifle.
I believe the act of the game spawning the newly painted gun which is supposed to be now located at your feet, is now spawning the gun 10-15 meters north of your location. I haven't tested it because i don't have any more paint.

Okay, found another mosin. I still had the one i painted black. removed all the attachments and removed the chambered bullet (had the mosin glitch). Painted it green and it did not leave my inventory ( now cammo). Well i don't have any more paint to try on the new mosin. Need try to paint the new mosin with no attachments or bullets to see if that reproduces the bug.