I don't think the fact that some of the chapters have organs that don't work properly anymore is the result of time. I mean, chapters such as the Utramarines, Dark Angels & White Scars still seem to have properly functioning geneseed and their geneseed is just as old as that of the Imperial Fist or Raven Guard. I think that's more to do with how the different chapters have handled, implanted and protected their geneseed rather than the passing of time.
It could be a massive conspiracy!
Maybe there is a traitor that is sabotaging the geneseed?
All that is important is known.