The 40 pence per mile (which i do) means you can't claim anything for the van as the it covers everything. They said you can't even claim for the cost of the van if you use the 40ppm as it's inclusive.
Yes, that is how I understand it too, except the figure I use is 42p a mile. 
I had always thought that the 40p (or 42p) per mile looked slightly but not overly generous but had not realised it included the van cost. Now it looks like a really bad deal. I suppose it works out alright if you are a very high mileage user but my business mileage is in the 9,000 - 11,000 miles per year bracket. It would only take one or two big repairs to leave you out of pocket I think.
Which garage do you use.
9000 miles * £0.40 = £3600. £1000 for Derv £200 tax and you are still left with £2400 to cover costs.
My derv bill would work out a bit higher than that I think but I'm often lugging a few hundred litres around in a Trafic van.
Also, bear in mind that the cost of the vehicle comes out of it. I paid 8 grand for a second hand Trafic so I think that 2 grand would be offset in year one. If my derv bill is a couple of hundred higher than you state (which I think is about right), that is £3,200 for year one. Then factor in £180 tax, £350 insurance and that comes to £3,730. That leaves me MINUS £130 to get it serviced and/or repaired PLUS the £50 MOT fee.
OK so in year two I would have an extra £500 to play with (capital allowance would be 25% of (£8,000 - £2,000) = £1,500 but as the vehicle would be a bit older that could easily be swallowed up with extra maintenance. Oh yes. Nearly forgot the tyres. Paid about £240 for them.
The taxman doesn't give stuff away when they try to set fixed allowances.
I'm still not convinced that I would have to accept the IR's 40p a mile anyway. It looks to me like there may be a bit of confusion here with self employed apportionment and employee usage.
I'll see my accountant soon to clear this up.