I like the partial build feature and want it to be kept active by default. However the state of this option does not seem to be saved as it is by default inactive as soon as eclipse is restarted. I am using eclipse 4.2. but experienced the same under version 3.7.
As I just noticed, it is automatically deactivated even after a certain time, say after an half hour, even if eclipse is not restarted in the meanwhile.
I can confirm this bug.
Those who are affected, could you please cross-check with Bug # 3586351 at
https://sourceforge.net/tracker/?func=detail&aid=3586351&group_id=133306&atid=726818
I.e. the "Build Partially" switch seems to be ignored entirely in my case.