The naive presentation of the transparent problem is circular, and for that reason ill defined (what you do depends on what's in the boxes depends on omega's prediction depends on what you do...). A plausible version of the transparent newcomb's problem involves Omega:

1. Predicting what you'd do if you saw box B full (and never mind the case where box B is empty).

2. Predicting what you'd do if you saw box B empty (and never mind the case where box B is full).

3. Predicting what you'd do in both cases, and filling box B if and only if you'd one-box in both of them.

Or variations of those. There's no circularity when he only makes such "conditional" predictions.

He could use the same algorithms in the non-transparent case, and they would reduce to the normal newcomb's problem usually, but prevent you from doing any tricky business if you happen to bring an X-ray imager (or kitchen scales) and try to observe the state of box B.