I'm not clear at all what the problem is, but it seems to be symantic. It's disturbing that this post can get 17 upvotes with almost no (2?) comments actually referring to what you're saying- indicating that no one else here really gets the point either.
It seems you have an issue with the word 'dependent' and the definition that Eliezer provided. Under that definition, E (the ith digit of pi) would be dependent on C (our decision to one or two box) if we two-boxed and got a million dollars, because then we would know that E = 0, and we would not have known this if we had not two-boxed. So we can infer E from C, thus dependency. By Eliezer's definition, which seems to be a special information-theoretical definition, I see no problem with this conclusion. The problem only seems to arise if you then take the intuitive definition of the word 'dependent' as meaning 'contingent upon,' as in 'Breaking the egg is contingent upon my dropping it.' Your symantic complain goes beyond newcome- by Eliezer's definition of 'dependent,' the pH of water (E) is dependent upon our litmus testing it, since the result of the litmus test (C) allows us to infer the water's actual pH. C lets us infer E, thus dependency.
Sorry, the above post omits some background information. If E "depends on" C in the particular sense defined, then the TDT algorithm mandates that when you "surgically alter" the output of C in the factored causal graph, you then you must correspondingly surgically alter the output of E in the graph.
So it's not at all a matter of any intuitive connotation of "depends on". Rather, "depends on", in this context, is purely a technical term that designates a particular test that the TDT algorithm performs. And the algorithm's prescribed use of that test culminates in the algorithm making the wrong decision in the case described above (namely, it tells me to two-box when I should one-box).
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.