Not sure if your still looking for an answer. But for someone else who has the issue and may find this. When I had this issue Fancy Block Particles was the causes of my issue like this. Also, with other mods when placing items caused them to become missing. For me when this is enable it will cause some blocks from IC2, Advanced Machines, Advanced Solar Panels to become missing when placed. Disabling the effects or deleting the mod should fix the issue.