The other issue report was marked as resolved, because it could not be reproduced, so I'm making this new issue report, with instructions for how to reproduce it. If that is not the correct thing I should do, I apologize. I also posted a comment with instructions on how to reproduce it in the original thread.

Steps to Reproduce:

1. Start a new Minecraft server
2. Run, fly or teleport around to generate a lot of chunks
3. Restart the server
4. Note the CPU and RAM usage
5. Shut down the server
6. Delete Mineshaft.dat
7. Start the server
8. Note the CPU and RAM usage
9. Compare the before and after CPU and RAM usage

The more chunks you generate, the greater the difference will be, and the weaker the hardware it's running on, the fewer chunks you will need to generate before you start noticing the lag.

On my hardware, I had to generate approximately 4000 region files before I started to notice the lag, and it was using close to 100% of my CPU, and 100% of the ram I allocated to it, no matter how much I gave it, with absolutely no one logged on to the server.

After moving Mineshaft.dat out of its native folder and restarting the server, 100% of the lag was gone. It was back to using virtually no CPU when no one was on, and only a few MB of RAM. When I put the file back into the folder and restarted the server, all of the lag was back.

Some people in the original issue report stated that they believe it might be continuously loading unoccupied chunks into memory, and once the allocated RAM is used up, Java's garbage collection maxes out the CPU, trying to free memory.