The Seventh Circuit's opinion in Aimster, formally known as RIAA v. Deep, is the one attacked on the "techie end" of the Internet, as it found a basis for liability by the "software provider." I'm not entirely certain that there is a conflict, primarily due to radically different procedural postures. In Grokster, the trial court granted summary judgment of nonliability to the software providers; that means that the Ninth Circuit reviewed the evidence in the record de novo, and had the freedom to interpret it as it wished. Based at least on the Ninth Circuit and trial court descriptions of the facts, there was little (if any) evidence (in the record, anyway) of intent to facilitate widespread copyright infringement. Aimster, however, came to the Seventh Circuit as an appeal by the software provider (Deep) against a preliminary injunction entered against him by the trial court. The Court of Appeals did not, and could not, review the record de novo; the factual record on a preliminary injunction is reviewed for abuse of discretion—a much more deferential standard. Further, unlike Grokster, the trial court's decision, and summary in the Court of Appeals decision, reflect significant evidence in the record of specific intent—or at least willful blindness—to facilitate widespread copyright infringement.
Willful blindness is knowledge, in copyright law (where indeed it may be enough that the defendant should have known of the direct infringement) as it is in the law generally. One who, knowing or strongly suspecting that he is involved in shady dealings, takes steps to make sure that he does not acquire full or exact knowledge of the nature and extent of those dealings is held to have a criminal intent, because a deliberate effort to avoid guilty knowledge is all that the law requires to establish a guilty state of mind. In United States v. Diaz, the defendant, a drug trafficker, sought "to insulate himself from the actual drug transaction so that he could deny knowledge of it," which he did sometimes by absenting himself from the scene of the actual delivery and sometimes by pretending to be fussing under the hood of his car. He did not escape liability by this maneuver; no more can Deep by using encryption software to prevent himself from learning what surely he strongly suspects to be the case: that the users of his service—maybe all the users of his service—are copyright infringers.
Aimster, slip op. at 11–12 (citations and parentheticals omitted). What is most important is that the law of "willful blindness" simply is not so clear in the Ninth Circuit, and that is not restricted to the context of copyright.
So, if there is a conflict, perhaps it's a conflict in procedure and rules of evidence as much as it is in copyright doctrine… or, perhaps, it's just that the facts are different. The point of having a judicial system is to allow for differing factual patterns.
Or, perhaps, there's a conflict in methods of statutory interpretation (like this Court is going to be able to resolve that cleanly, especially after Thursday's opinion in the diversity-jurisdiction cases). That, however, is for another time.