You should have used a rust conversion coating instead of removing surface rust.
Naval Jelly contains acid that dissolves rust, but it will not work through paint.
It is also likely to kill just about any plants in the immediate area.
If there are only a few spots sanding and spotting is probably the best choice.

I painted a near totally rusty shed ten years ago.. it gets sprinkler misting at least weekly right now. It had been misted twice weekly by the sprinklers until they made sprinkling restrictions tighter at once per week about a year ago.
It has only a couple spots of rust peeking through now.

Brushed on two coats of Ospho, which is about the consistancy of water. Basicly a weak phosphoric acid with some lanolin in it. It converts the rust to sort of a phosphate primer. Lanolin is one of the worlds best rust preventitives.
Then I brushed on two coats of Rustoliem cream colored paint. Added some blue paint for trim detail... done.