When you say the same two parts turn black every time, do you mean identical parts, or two parts in every load but not necessarily the same type of part? If it is identical parts, then yes it may be the type of aluminum, there are some types of aluminum that are difficult if not impossible to anodize nicely. Cast aluminum is generally in that category, and some types of wrought and extruded aluminum alloys have various undesirable quirks also.
I haven't personally anodized any cast, although I have had it done in the past. From what I am told, a smooth polished cast surface before anodizing may help. I don't know if that is true or not, but it might be worth checking out. I also believe I have read where some of the Japanese aluminum is worse, but again I don't have any personal experience to call on.
On the other hand, too much current can blacken parts, and it's actually called "burning" the parts. So if it was randomly happening to various parts and the alloy didn't seem to be the common denominator, I might suspect the connections or current density might be bad.
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