Sorry to hear that.

But what you really should have done is to send the petition again with the new checks on 9/28,not only the checks. Now I am sorry to tell you, you can do nothing to correct it.How possible for the INS to relate thoese three isolated checks with tons of petitions? Impossible. You should have included the check with the petition again. But now it is October already, you can't file I485 concurrently with I140. You still can file your I140,though.

I am surprised to see such kind of mistake made.You have to bite the bullet.