To get round this problem I published a paper in which we developed new algorithms for parsing fixation durations. These algorithms can be downloaded here. Using these is pretty tricky, though – as the settings are very dependent on which exact eyetracker you’re using. And there are lots of other researchers, such as Roy Hessels at Utrecht, who have done great work since we published these algorithms – with results that are, honestly, probably better than ours!
Feel free to email me if you’ve got any questions about this though – or reach out through my contact page.