This file contains 5 saves of the same fort over time. The initial embark had Tower and Fortress listed as neighbors. The main bug comes from the lack of invasions after an initial invasion. The timeline spans about 5 years or so. Several other potential bugs or weirdness is listed.

The .zip contains four folders with the save file for each. All but "IronBow" and "HumansListed" were saved on 0.40.04, which were saved on .05.

First folder (chronologically) - Dwarf Attack

Fortress was listed on the neighbors screen. This save occurred during an attack by dwarves on this player fortress. Checking legends it seems that the "Sack of Merging" dwarven group of the Entangled Oil attacked the Crystalline Papers of The Entangled Oil at Theaterunited. Not sure if this is a bug.

Second - Zombie

Zombies from the tower show up at the fort.

Third - Post Goblin

I only saved after the zombies finished off the goblins (siege by the zombies eventually ended, but the zombies stuck around). No goblins are listed in the civilization screen. Also, one of the goblins died from his skull being crushed by a sock. Not sure if this is a bug.

Fourth - IronBow

Zombies are dead. Only the dwarven settlement and the elven settlement are shown in the civilizations screen - no goblins are listed. The dwarf at the coffin (on the initial screen on load) is trying to pick up steel bolts (which are lying on the coffin), despite having an iron bow. He is unsuccessful. Not sure if this is a bug.

Fifth - HumansListed

Humans now appear on the civilization screen (trading with the humans has happened). A forgotten beast and mountain titan have already arrived. No invasions apart from the initial dwarven, zombie, and goblin attacks have ever happened. No goblin snatchers. Also, one kobold arrived at some point early on.

Related to: Bug Tracker: 0007739

Discussion Topic (very similar to this situation): http://www.bay12forums.com/smf/index.php?topic=141422.0