The rim can be true side to side (i.e. vis-a-vis the brake pads) but you may have a flat spot in the rim. You would be able to see it buy doing what I describe in post #8 of this thread, focusing on the rot the tire. If a portion of the rim looks like it's rising towards the hub, that is a flat spot in the rim. That's a rarer cause than an improperly seated tire. You may also have a bulge in the tire due to damage or a defect.