Since our server updated to Spigot 1.8, we noticed that the server started receiving considerable lag. According to /timings paste (here), we found that it was caused by a large amount of entities, though we have never had this problem before in the 2 years we have been running. We run a 32 GB RAM server with overclocked i7 processors and SSDs, we have never had a problem with lag, besides mass land generating and worldedits.
We checked how many chunks were loaded and found that we had over 60,000 chunks loaded in our main world (with 10 players on, we normally would have about 10% of that), with a total of 70,000 chunks loaded. I understand people were exploring the map, as we had expanded the borders, but 70,000 chunks is rediculous impossible unless chunks are not unloading like they should be. We tried restarting the server multiple times, but the problem still persists. Restarting is the only way we found to reduce the chunks.
I have no clue how long it would take to resolve this issue.