Apparently this hasn't been marked as answered, so I'll try and answer your question. Alchemist is almost certainly right, you need to press the green button when you run an experiment, not the blue or grey one. Also, if you want, you can take a Kerbal on EVA to go take the data from the module. This renders the module inoperable, but it still gives you the ability to recover the data, and you don't even have to keep the science part. I would suggest getting the Science Revisited mod, it makes more sense in terms of progression.