1.6.1 - 1.3 server lag

Put the summary of the bug you're having here

What I expected to happen was...:
Nothing at all, I was expected the server work

What actually happened was...:
After a few stop / open, the server wont work anymore, it say that it's in 1.3 version.

Steps to Reproduce:
1. Start a server on linux ( Survival )
2. Open, close it a few times
3. Try to connect to the server and connect into the server