Scanning with Canoscan 9000f

I have bought a few days ago CanoScan 9000f and already have some problems (not that I wasn't expecting them).

The first thing is that all of my photos are coming out somewhat darker than expected so I am wondering if it can be resolved during the scan rather than in the post process? And while at it, how can I get the most of the negative, in terms of getting the highlights and shadows? While printing the same negative in the darkroom I am getting better results with some fresh chemicals and pretty outdated papers...

Also, the scanner is cutting away portions of the negative and I (of course) have no idea why. I bought this scanner because I was not satisfied with DSLR scanning, I sure hope that it doesn't come out to be my mistake for doing so...

Scanned with Canon software from the box, Canon MP Navigator EX 3.1.

I have this scanner and am very happy with it for what I use it for - which is mainly for posting on the internet. Originally I was going to use it in place of contact seets, but I find it faster to make a traditional contact sheet. I do have to fool with the scans in Photoshop Elements however.