Rust never sleeps. There is no direct connection between the water jackets and oil system, so don't worry about that. But I guess there is still flaky rust in the system that is coming loose as you run the engine. Yes, I would go back to flushing and maybe add a cleaning agent. I use Cascade dishwashing detergent. Just don't let it sit too long as it is so aggressive it may find weak spots in your radiator. It also is harsh on aluminum so the timing cover may be attacked. The water pump is new so it should be OK. Just let it get good and hot, cool down, drain, and flush, flush, flush.