I recently ran into the problem that I have a common library where i store all my Bibtex references, but Eclipse/Texlipse refused to find it, although I linked the library file from within the project folder.
The solution is rather simple, as it just requires setting the BIBINPUTS evironment variable, so Bibtex can find the desired *.bib file at the different location.
To do so in Texlipse, go to Preferences->Texlipse->Builder Settings->Environment. There you hit ‘New…‘, enter ‘BIBINPUTS‘ as the key and the directory where the bibtex library file (i.e. your *.bib file) is located as the value. Hit OK, close the preferences screen and you are set.
Hope that helps.