I am not sure but I think that the issue with \cite is back when using multiple files.(https://sourceforge.net/projects/texlipse/forums/forum/451977/topic/4847234)
I am using a master TeX document and \include the other files.
It may be related to the fact that I am using bibtopic and thus have multiple bibliography files.
The bibliographies are loaded at the end of my document.
Any tips or confirmation would be very mch appreciated.