Either to protect the authors of the original software to check if the warez group got the full algorithm or if they have something mildly different from the original that allows the authors to detect a keygen in newer versions, or because the warez group wants to make life more difficult for copycats... or, and I've seen my fair share of that (and earned good money to clean up), a third party wrapped a highly popular keygen like for Adobe CS6 in some sort of malware and wanted to avoid detection.