Hey,

I have finished Fallout 1 not long ago and I think it is a great game. But I was really confused about the ending.

Well, when I finally destroyed the Master, the ending cutscene shows that Shady Sands and the Hub were destroyed and Necropolis was build up by the ghouls again. Which suprised me because both, Shady Sands and the Hub were still populated and not over run by the mutants when I visited them last time. I have checked that with my latest save game and this was nearly at the end. And funny thing: Necropolis was now populated by the mutants. So how could they build up again?

Is this somekind of bug or something else? I have heard the time limit lies now by 13 years or so. The original time limit there was 500 days. So, is that maybe the reason why I got the "bad" ending? I finished all quests and acted like Mr. Nice Guy all the time.

Had anyone else this problem?

You could have a look here:
http://fallout.wikia.com/wiki/Fallout_endings
and see if you did any of the things to trigger a bad ending. In Shady Sands for example, if Aradesh and Tandi are somehow killed, then it triggers the bad ending. In the hub, failing to complete a specific quest, and/or doing one of the Decker quests also triggers a bad ending.

Ah I see now, look at the bottom entry at Shady Sands. If the master is still alive after 230 days, then Shady Sands gets overrun by mutants in the end. There are several other endings that are also affected by the Master surviving for too long. So perhaps check in your saves how many days had passed by the time you confronted the Master. It indeed seems to be inconsistent with those places still being seemingly ok by game end, but I suppose it could be reasoned that if the Master survives for too long he amasses an army large enough that there are enough left by the time of his demise to still wreak havoc across the landscape, or something like that.

Well, I killed the Master ingame at the 26th January 2163.

Yeah, so that is long enough to trigger those bad endings. The game starts in December 2161
http://fallout.wikia.com/wiki/Timeline#2161

But why is Junktown still alive? And wasn't there a patch where the timeline should be changed?

Uhm, I can't really say. Perhaps that wikia isn't wholly accurate wrt junktown.

I find gamebanshee.com to be extremely thorough and helpful with their guides, maybe it will give you some answers.

Hm, maybe I just got over the time or something else. Maybe next time I got the good endings for all places.