There is a long thread on these boards somewhere where I had a similar situation a couple months back with a new sub. Like Mark says, a lot of this can just be the way the waves are acting in the room. I expect Neon to jump in here any minute and he can give you specifics about where you will have problems with certain frequencies, which depends on your room size. For me it was in the 60 - 70 hz region, and 90 - 95 hz region.
Long story short, it took a lot of messing around with placement and seating position to get it as good as possible. Obviously you want the graph to be as flat as possible. You are finding out why many people run two subs, as this definately helps flatten things out. All you can really do is try positioning changes and try again. Even the direction the sub points does make a difference. I tried the exact same spot with the sub facing 90* differently, and the second attempt gained 28 db (!!!) at some frequencies.
Good luck
Edit: I just remembered too that some receivers will need a 10 db boost in output if you are using the analog ins. Some have it or apply it without you doing anything. I don't think this is an issue if you have some frequencies where the sub is too loud, but I thought I would mention it.
