"So correct me if I'm wrong - HPE's argument is that Lynch's counter suit has been made against Autonomy even though it was HPE making the statements. Which is fine I guess, Lynch should sue the correct people. But then, why are Autonomy the ones suing Lynch and not HPE? Since it is HPE who are the ones that lost money, not Autonomy. So if the correct people were suing Lynch, he would be countersuing the correct people. Seems pretty clear to me..."
As I understand it, the problem is that the entity suing Lynch did not previously exist. As the article notes, it's not actually Autonomy suing Lynch, since it no longer exists, but rather ACL Netherlands BV, which it the subsidiary set up by HP containing all the assets they acquired from Autonomy. The statements Lynch is suing over, on the other hand, were made by HP before ACL Netherlands existed. So the argument goes that he can't be making a legitimate counterclaim, because the entity suing him did not exist when the comments he is suing over were made.
The problem comes with the specifics of what a counterclaim is - it's a claim made by the defendant in a lawsuit specifically in response to that suit, and in which both suits are resolved as a single case. Lynch could start an entirely separate case against HP if he wanted to, alleging that their defamation harmed him, and that would be fine. But because he's brought it specifically as a counterclaim to an existing suit against him, it becomes quite important exactly which entity is suing him and which made the comments he wants to sue over.