A number of people complained about performance problems in GanttProject 2.0.4 so I have spent last two evenings on profiling.
In one case the problem was in the project file: I found there one task that started in year 0007 (yep, 2000 years ago) and was half a million days long. It must've been an effect of this UI problem related to entering years using short notation ("7" instead of "2007").
In the second case the problem was in a code doing a lot of unnecessary stuff when loading a project file. Changes were quite easy and small and in the end I successfully loaded a project consisting of 1500 tasks and was able to work with that project with no significant pain.