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:
For D to depend on C means that if C has various logical outputs, we can infer new logical facts about D's logical output in at least some cases, relative to our current state of non-omniscient logical knowledge. A nice form of this is when supposing that C has a given exact logical output (not yet known to be impossible) enables us to infer D's exact logical output, and this is true for every possible logical output of C. Non-nice forms would be harder to handle in the decision theory but we might perhaps fall back on probability distributions over D.
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.
...reasoning under logical uncertainty using limited computing power... is another huge unsolved open problem of AI. Human mathematicians had this whole elaborate way of believing that the Taniyama Conjecture implied Fermat's Last Theorem at a time when they didn't know whether the Taniyama Conjecture was true or false; and we seem to treat this sort of implication in a rather different way than '2=1 implies FLT', even though the material implication is equally valid.
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.