Still sounds a bit heavy. After 2 - 3,000 miles your engine should have relaxed a bit, and you'd see an improvement in consumption.
I'm doing the same as you, and get a pretty consistent 55mpg - that's based on miles/fuel added, not that daft trip computer. I assume you're not using that for your numbers?
If you're really getting such bad figures, I'd think about the following;
- Brakes sticking? Unlikely, but if they were they'd have an effect.
- Tight chain? As above, but check it anyway.
- Tyre pressures - are your tyres properly inflated, if not, get it done! 33 front, 36 rear.
- Is it just the way you ride? I don't know whether you're an experienced rider or not, but maybe try a little experimentation. Try riding with economy in mind, this doesn't mean never going over 2,000 rpm (and should never be a priority over safety), but give yourself an extra 10 minutes each morning for a week, and try slowing down, thinking carefully about what's in front, and anticipating changes in speed, stuff like that. You can make a noticeable difference, especially if you're normally heavy handed.
I've done this on most of the bikes I have owned, sometimes to the point of irritating myself, but it's good to know how to save fuel, for when it hits £1.80/litre . . .!