Could be that your sensor is getting has picked up a few bits of dust or gunk.
Since it is a digital rig, it may be worth doing a white wall test with a few lenses -
Photograph an evenly lit wall with a few different settings, with a reasonable exposure. Wide open and stopped way down, and then with a few different lenses if you have them. If the spots are showing up in the same spots across different lenses, then you know you should be looking to your sensor. If they show up only with one lens, then you know that is your problem.
But another good point to look at: Double check you're not applying some weird pre-set to the images on import. Traced a friend's problem back to them accidentally applying some manual spotting work from one photo to all of their photos. Needless to say an overlay of spotting for a specific photo probably isn't all that helpful in the vast majority of other photos.