Now that the trick is revealed, I think I have to give an explanation here before someone asks "how do you decompile a swf".
So yes, I used a decompiler to look at the source code and to extract some pieces of information from it that weren't well known (drop rates, mutation effect, AI algorithm, ...)
Inside the source code, I spotted half a dozen bugs that I wrote in the wiki page and I also found a few major security holes. Chances are high that those holes are the ones abused by cheaters to get a score in t50 ten minutes after their account creation.
I wrote to Zanzarino immediatly to offer my help in solving those issues. But for now, I got no answer.
So I ask everyone who has some knowledge in engineering NOT TO give advices on how to decompile and how to read an actionscript code until those problems are fixed.
I hope you understand that having a "cheater free" game is more important than anything else.