Manual vs. Auto focusing

I've been experimenting with photographing mountain sunrises recently. My
concern is that I've tried to utilize the automatic focusing of my 18-55 Nikor
on my D5000 and most of the background is not in focus. Granted, lighting at
that time of the morning is not good before the sun comes over the horizon, but
I was looking for the glow on the mountain.

After looking at about 150 photos that were mostly not in focus, I went back
to the same area and tried to take photos using the manual setting. It seemed to
work better but a lot of photos were still not in focus at the farthest
point.

My concern is aimed at the possibility that the lense may not be functioning
properly under these conditions. Sure works great in total sunlight.

Any thoughts from any of you owning a D5000 and a 18-55 Nikor?