The first time, the Jackal had a fit of sentiment and stuffed him into a regeneration chamber. The second time, he left behind an actual corpse that was later revived (whether by the Other or by the Jackal, it was somewhat ambiguous) and further mutated into the "Tarantula" in Spider-Island. The third time, he was literally eaten by mutant werewolves and explicitly revived by the Other. The fourth time, the Other spat him out of its corpse. Maybe there was a fifth, but I'm blanking on that right now.
The spider is always on the hunt.
The "perfect clone" thing never quite made sense. It seemed to be designed to make Ben seem more important and later Peter when he was thought to be a clone integral to Jackal's master plan.
It seemed to be contradicted by the idea that Ben had researched into clone degeneration and was convinced it would eventually catch up with him. Likewise when Peter was portrayed as the clone he too was concerned about degeneration and at one point it seemed to be happening to him when he was dying in hospital which led to him getting his powers back.
Of course dying doesn't automatically mean degenerating. The random clone found in the smoke stack didn't degenerate and on the flip side degenerating did not necessarily mean death as Spidercide was basically a puddle of goo when Scrier brought him back to life.
My No Prize solution would be that all the repeated and extreme physical damage he received in PP:SM#75 (brutal beatings, bombs, falling off a skyscraper on to a car) broke something in his clone metabolism and triggered a premature breakdown of his cells. The reason why he didn't degenerate in SS#25 (still can't get over how bad that issue was) is because he's now a New U clone and they're genetically more stable than Miles' original batch. It's not a great explanation, but it's the best I can do.
Ben degenerating in PPTSSM 75 wasn't internally consistent, but was probably seen as a necessary evil to 100% confirm Peter as the original. That's the only reason it happened IMO. It does leave a huge opening for them to reveal that the clone who Norman killed wasn't the real Ben.
I'm seriously liking all of these "true Ben" theories, Marvel I hope you're listening/reading this (and for added measure make NuBen Spidercide)
The city I once knew as home is teetering on the edge of radioactive oblivion
Glad we could help.
spoilers:end of spoilers
So far, it seems Gage over in Spider-Geddon #3 is completely disregarding the end of this issue/series, insofar as how Ben's acting, unless it's just that --- an act, and he's gonna go nuts all over again to justify Otto/Superior Spider-Man dispatching him.
The spider is always on the hunt.