In the setup in question, D goes into an infinite loop (since in the general case it must call a copy of C, but because the box is transparent, C takes as input the output of D).
In Eliezer's similar red/green problem, if the simulation is fully deterministic and the initial conditions are the same, then the simulator must be lying, because he must've told the same thing to the first instance, at a time when there had been no previous copy. (If those conditions do not hold, then the solution is to just flip a coin and take your 50-50 chance.)
Are these still problems when you change them to fix the inconsistencies?
In the setup in question, D goes into an infinite loop (since in the general case it must call a copy of C, but because the box is transparent, C takes as input the output of D).
No, because by stipulation here, D only simulates the hypothetical case in which the box contains $1M, which does not necessarily correspond to the output of D (see my earlier reply to JGWeissman:
http://lesswrong.com/lw/1qo/a_problem_with_timeless_decision_theory_tdt/1kpk).
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.