Avid BB7 brake disk problem

I have a slight problem with my Avid BB7 road disk brakes.
This is the first time I’ve had disk brakes so I’m not that familiar with how they should feel compared to rim brakes. Before I start I should say that I’ve had these brakes ( and the bike) a week now and the pads have been properly bedded in. I’ve also consulted several sources on how to set the brakes up (including Avid’s .pdf file) and I’m confident that I’ve set them up correctly.

The problem I’m experiencing is that when I’m applying the brakes, it feels like the pads are biting the rotor more positively in some places on the rotor than others. In other words, when I grab a handful of brake it feels slightly juddery and not smooth and consistent like my rim brakes used to. I often feather the brakes on long downhills to just scrub off some speed and it feels like the brakes bite strongly for a second and then less strongly for a second and so on. In other words, the breaking isn't consistent. The same happens when you want to stop quickly and grab more brake: only it’s more pronounced.
I’ve tried cleaning the rotors with disk cleaner and I’m pretty confident that the rotors are true. I’m at a loss to figure out what it might be. I haven’t actually inspected the pads yet, so maybe this should be my next step.
Can anyone throw any light on this problem?
Many thanks

I’ve tried cleaning the rotors with disk cleaner

Disk cleaner is, in my experience, one of the worst things you can put on a disc brake.

I'd get the pads out and remove the surface layer with some fine wet n dry on a flat surface then refit, ride around with the brake dragging then douse the entire disk and caliper with clean water, repeat a few times for each brake, repeat the sanding the pads step and I'd expect that would improve things.

if the disc's and pads haven't been worn in then i guess there might be a lack of braking / uneven braking
i was told to ride along with your finger covering the brake and let the pads heat up / disc's heat up
once you've done this a couple of times the brakes should bite much better and possibly more consistently

thanks for the tips .
I've been riding the bike for a couple of weeks now (about 200miles) and the problem persists. I'll have a go at sanding the pads and see if that helps.

cheers
ives