Dimitris,
That's an interesting question. By default, especially if you're using prepared questions, the vote results should stay with the flipchart you're using and be separated by flipcharts. I'm not able to replicate your results.
I'd be curious to know if you go into File- Settings- Learner Response Systems what options you have checked, especially for Append Question to current flipchart and Import Questions to New Pages, and to confirm you're using the green button for your prepared questions. You might try to set the former setting on and the latter off. Failing all of this, you might also save your results between flipcharts and close the software and re-open between flipcharts.
I'm logging this against case 00362089, please let us know your results.
Thank you,