Server Chunks not saving

While playing on a server, I have changed multiple blocks and moved some villagers around. I left the chunks via the nether and came back. The area I came back to was the same as before I changed it. However, I had the items that I had picked up off the ground and they were still in the same spot.

Issues:
Unable to change the chunks as they come back to what they were in 1.6.4.
Duplicating items that were there on unloading chunks and relogging.
Can repeat