Pad material gets transferred to the disc surface. Sounds to me like you may have either uneven transfer or there has been some contamination. The solution to that is to thoroughly clean the disc surfaces with brake cleaner or possibly even an abrasive to cut through any surface deposit.
If there is stubborn visible rust then you will find it difficult to get even braking. Discs from motor factors (in the UK anyway) are not expensive and should be considered to be consumables.
You then benefit from doing a proper brake bedding procedure, do repeated braking from progressively higher speeds while increasing the braking force each time, gentle to begin with working up to quite hard braking. They really need to get quite hot to properly bed-in. You can find this procedure described on various websites. Normal driving doesn't usually reach these conditions.
It could be that the pads are too hard for road use, competition pads are usually not good for light use as Culzean says.
It is of course possible that the discs are not true, or the hub face on which they sit is corroded or not flat. Careful examination will show this, if you suspect the disc run-out it needs a dial gauge setting up to measure it, and use a micrometer to measure the thickness round the disc to ensure it isn't uneven.
