I am a scientist. Although I mostly do computational/theoretical work, I have a lot of colleagues who are chemists, geologists and biologists. Just like the scientists in your question, these people spend only a small part of the year on location gathering data. For most of the rest of the time, we are in our institute/spaceship engaged in one or other of the following activities:

 * analysing samples in the laboratory (the samples may have been gathered some time ago)
 * analysing data from the lab results
 * formulating hypotheses to explain the results
 * constructing mathematical or computational models of the results
 * giving or attending seminars, discussion groups etc. so that we can understand each other's work
 * writing scientific papers so that our results can be understood by the wider scientific community
 * perhaps doing some media outreach work to present our results to a popular audience as well
 * teaching
 * writing grant proposals
 * doing administrative paperwork, of which there is a surprisingly huge amount

The last three may or may not be relevant on a spacecraft, since there might not be any students on board, and one would hope (optimistically) that most of the admin stuff would be done elsewhere. But the other things would be relevant parts of your scientist's work. I would expect the spacecraft to have an on-board laboratory, so scientific work doesn't have to stop as soon as you leave the planet. 

But the results dissemination and paper writing would also be an important part of any scientists' time on a long-term mission. After all, if you don't tell anyone about your results, there wasn't much point in doing the work in the first place - and who better to write it up than the people who are out there in the universe making the observations first-hand? This is one of the most important parts of a scientist's job, and the travel time between planets would be a welcome opportunity to do it.