Server running without any base files

The server does not (re)generate server.properties

I tried to change the server port to 25595, but nothing happened.

What actually happened was...:

It still ran on default. It also does not generate whitelist files and the like.

Steps to Reproduce:
1. Erase everything in server directory
2. start the Minecraft server.
It runs normally, but no files are created

Log:
[12:31:18 INFO]: Starting minecraft server version 14w26c
[12:31:18 INFO]: Loading properties
[12:31:18 INFO]: Default game type: SURVIVAL
[12:31:18 INFO]: Generating keypair
[12:31:19 INFO]: Starting Minecraft server on *:25565
[12:31:20 INFO]: Preparing level "world"
[12:31:20 INFO]: Preparing start region for level 0
[12:31:21 INFO]: Preparing spawn area: 2%
[12:31:22 INFO]: Preparing spawn area: 25%
[12:31:23 INFO]: Preparing spawn area: 71%
[12:31:24 INFO]: Done (4.004s)! For help, type "help" or "?"
[12:31:27 WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 2335ms behind, skipping 46 tick(s)

Nothing out of the ordinary, except said problem.