Here's the THUNDER story as far as I've been able to piece it together from (scans of) the original books and (the database of) Copyright Office records...
The interiors of the Tower THUNDER Agents comics have no copyright notices.
The first issues of each series DO have obscured, hard-to-read copyright notices on the covers. That's technically permissible (today), as book-form works may print it on "either side of the front or back cover." However, there are two problems.
First, they're obscure and hard to read, as mentioned. With the exception of UNDERSEA Agent, which has the notice where you'd actually find it, the rest hide the notice within the art, in dark colors. "The notice should be permanently legible to an ordinary user of the work under normal conditions of use and should not be concealed from view upon reasonable examination." (NoMan #1 is another outlier: It has a hand-written notice hidden in the art that I can't read.)
Second, for periodicals, the rule as of 1965 was, that the notice must be "either upon the title page or upon the first page of text of each separate number or under the title heading." That's not the cover, which makes these notices invalid. There's good reason for that, too: A cover notice often claims copyright FOR the cover as a separate work.
This last has changed in the intervening years. Front and back covers, inside and out, are currently valid places for a copyright notice. However, they got it wrong on publication, and you can't get things back from the public domain.
So those were the '60s. The original books, hands down, have no copyrights. If Tower owned the copyright to anything in the entire series, it's the cover to UNDERSEA Agent #1.
Enter John Carbonaro (whose pasta sauce I love...), who "buys the rights." Like everybody in the comic book industry, he had absolutely no idea what that means or what he bought, and assumed it involved exclusive rights to "characters," which really isn't a legally-defined concept. His partner Singer actually did the research and determined that, no, there were no copyrights to own, so he split off.
Now, Carbonaro's interpretation of the copyright law is wrong, but understandable. By 1980, the law had changed to allow copyright notices more globally, as I mention above. As a complete novice, he naturally applied current law to old works and got the wrong answer.
Anyway, when Singer tried to publish his own series, Carbonaro tried to sue, but learned that you don't have the right to sue without a copyright registration. Therefore, he registered those books with (bad) copyright notices. If you look at the Library of Congress records, you'll see that THUNDER Agents #1 is registered, but not until September of 1984. The rest of the registrations (minus NoMan #1, which I guess means that scribble wasn't a copyright notice after all) come in December.
From here, what I know only comes from secondary sources. Allegedly, Carbonaro brought Singer to court, and the judge ruled from the bench (i.e., without bothering to go to trial) that the original books were in the public domain, and Carbonaro had no case. Singer's announcement then caused a flurry of THUNDER appearances through the '80s, because, hey, public domain.
The case also caused Carbonaro to license the Agents to several small companies, hoping that the license agreements would bolster the view that he owned the properties.
Some time after that...I don't understand it at all, but Carbonaro apparently claimed that he petitioned the courts to "give him back" the copyrights, and allegedly succeeded because nobody contested it. But that's complete nonsense, since there's (as I said) no provision for retrieving the copyright of a public domain work. Otherwise, I'm sure somebody would have "re-copyrighted" the works of Shakespeare, by now.
However, since then, it looks like most of the industry has just played ball with Carbonaro, rather than worry about needing to fend off lawsuits from what seems to amount to an overly-posessive nut. Now that he's passed away, though, we'll see what happens. I can't imagine that his estate will be quite as obsessed with the characters.