Let me say I have nothing against Cloanto, I bought one copy of Amiga Forever and was gifted a newer one by a friend.
I have to agree, Cloanto is on shaky ground.
Just because they have a license to distribute, I don't believe that gives them the ability to file DMCA claims for instance. That is a right the copyright holder has and (I think) it's legally punishable to file a DMCA notice on copyrights you knowingly don't own.
If they are just reporting to your ISP that you are making pirated software available, that's legal, but kind of a dick move given the current state of things.
I'd like to see who really has the copyright, it's a shame you almost have to bait people into court to prove it.