I had this occur, and it was a monster of my own doing. The first thing I would look at is where you sanded the area that you assumed was somehow unevenly being grabbed by the brakes. I sanded a rim once, and I was careful to boot, but it created this incredible grabbing that was far worse than it was before.
The next thing I would look at would be the alignment of the rim brake calipers. be sure the mounting nut is secure and tight,and that the brake pads sit roughly equidistant from the rim.
When I true a performance road wheel, I settle for a single mm of lateral play. Not one of my customers has complained nor can I tell the difference. I doubt that it is an alignment issue. Pro mechanics go for 0.5mm lateral play, but hey...there professional racing mechanics.
And one more thing to check is that there isn't a loose spoke. Wheels are very strong and can survive a loose spoke. That spoke will compress excessively and loosen moreso at the top/bottom of the wheel rotation. This will create a temporary warp in the rim, and will also occur very close to the brake pads contact point on the rim. I had a set of Zipps that did that and it drove me nuts till I caught it during an inspection.
Hope it helps. Good luck!
Another weak point on a rim is where the valve stem protrudes. Does it occur there?