Thank you very much for the additional information.
Let me start by addressing your second remark regarding hierarchical layout reverting to the less efficient result. That is the intended behavior. If the options "Selected Elements Incrementally" and "Use Drawing As Sketch" on tab "General" are turned off (which they are by default and which they should be for first time arrangements), the positions of elements prior to the layout calculation have no effect on the result.
What you can do, though, is the following: Run the hierarchic layout with "Selected Elements Incrementally" and "Use Drawing As Sketch" turned off, then manually move elements to more favorable positions (does not have to be pixel-perfect), then run the hierarchic layout again but this time with "Use Drawing As Sketch" turned on. "Use Drawing As Sketch" will try to respect relative positions from the input graph. In other words, if you turn on "Use Drawing As Sketch", "Har 85" will stay between "CoL 85" and "Ea 85" for the second layout calculation (its exact coordinates will be changed, though).
That said, the two-pass approach is not necessary for your example graph. In your case, it suffices to increase the "Maximal Duration" for the layout calculation. By default, the duration is set to 5 seconds. Increasing that to 60 seconds, I got this result. The algorithm did not even run noticeably longer with the increased duration. So, why did this help nonetheless? Hierarchical layout runs in separate phases and we conducted empirical tests to determine for each phase its "typical" percentage of the overall runtime. The maximal duration is then split among the phases according to their typical percentages. In your case, the edge crossing optimization phase seems to require more than its typical share of runtime, while other phases require less. Increasing maximal duration allowed the edge crossing minimization to calculate a better result without increasing runtime for other phases.