I think this problem is based (at least in part) on an incoherence in the basic transparent box variant of Newcomb's problem.
If the subject of the problem will two-box if he sees the big box has the million dollars, but will one-box if he sees the big box is empty. Then there is no action Omega could take to satisfy the conditions of the problem.
The rules of the transparent-boxes problem (as specified in Good and Real) are: the predictor conducts a simulation that tentatively presumes there will be $1M in the large box, and then puts $1M in the box (for real) iff the simulation showed one-boxing. So the subject you describe gets an empty box and one-boxes, but that doesn't violate the conditions of the problem, which do not require the empty box to be predictive of the subject's choice.
I drew a causal graph of this scenario (with the clarification you just provided), and in order to see the problem with TDT you describe, I would have to follow a causation arrow backwards, like in Evidential Decision Theory, which I don't think is how TDT handles counterfactuals.
According to Ingredients of Timeless Decision Theory, when you set up a factored causal graph for TDT, "You treat your choice as determining the result of the logical computation, and hence all instantiations of that computation, and all instantiations of other computations dependent on that logical computation", where "the logical computation" refers to the TDT-prescribed argmax computation (call it C) that takes all your observations of the world (from which you can construct the factored causal graph) as input, and outputs an action in the present situation.
I asked Eliezer to clarify what it means for another logical computation D to be either the same as C, or "dependent on" C, for purposes of the TDT algorithm. Eliezer answered:
I replied as follows (which Eliezer suggested I post here).
If that's what TDT means by the logical dependency between Platonic computations, then TDT may have a serious flaw.
Consider the following version of the transparent-boxes scenario. The predictor has an infallible simulator D that predicts whether I one-box here [EDIT: if I see $1M]. The predictor also has a module E that computes whether the ith digit of pi is zero, for some ridiculously large value of i that the predictor randomly selects. I'll be told the value of i, but the best I can do is assign an a priori probability of .1 that the specified digit is zero.