When I build my project I get this error.
Serializing CDT Project settings has encountered a problem (Null Pointer Exception)
I am using latest
After spending a few hours trying to figure out the same error message this morning (along with a bunch of nondescript nullpointerexceptions from Eclipse) I compared the Eclipse project files with previous version and found that Eclipse had added an extra node to my .cproject file, making it three in total. I removed this one, which was the one added by Eclipse and also the last one in the file.
After removing that and restarting Eclipse everything was working again.
I hope this helps someone. I'm not sure whether this was unique or something that causes issues for others, but clearly the error points towards a CDT problem and therefore comparing the .cproject file to previous versions (or default ones) for changes is worth a shot.