Another log here:
myname@nbdeka1:/myname/data/downloads/factorio$ ./bin/x64/factorio
0.000 2018-01-22 22:08:21; Factorio 0.16.17 (build 35127, linux64, alpha)
0.043 Operating system: Linux (Ubuntu 17.10)
0.043 Program arguments: "./bin/x64/factorio"
0.043 Read data path: /myname/data ...

Downloaded factorio_headless_x64_0.16.15.tar.xz and factorio_alpha_x64_0.16.15.tar.xz,
starting ./bin/x64/factorio and ./bin/x64/factorio --start-server path_to_save.zip and connecting via localhost or in matching server after configuring.
Hosting in multiplayer trough factorio works without ...

Of course, attached it.

Yes, still happens in 16.15, attached desync reports.

The Map was created in 0.15 and played only in single player. Hosting in multiplayer trough factorio works without problems,
but as i put the map on a headless server on the newest version, the desync appears either instant or after some seconds.
Problem exists even in a fresh headless server and ...