Is it possible that the grains of sand are too large to get the deepest rust out? If that's the case, try one of these 2 options. These are what work for me.
1. Get some DuPont 5717S acid and use it full strength on the stubborn spots. Lay a cloth or paper towel over the spot and saturate it with the acid. Let it soak 15-30 minutes and then scrub with a wire brush or scrape with a very fine pick. I even use the corner of a razor down in the pit to break it up after it has soaked. Repeat the steps as often as needed until it dissolves the rust spot clean.
2. Use an extra fine grade of sand, mixed with 50% bead blasting media (any type or grade) in your blaster. Even worn out media will do the job. At work I save all of the old media from the bead blaster just for this purpose. I run it through my portable sand blaster for stubborn deep rust or spots on large panels that may warp from the heat of sand. Just don't use any that has been used on greasy parts because it is contaminated.
Once the rust is gone, it won't matter what filler is used, but the All Metal should be fine.
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