I see this behavior, too. Comparing a clean build from within Eclipse (BTW that does not reliably run bibtex and the two additional pdflatex-runs I need) with a manual run on the commandline: There are warnings listed in Eclipse's "Problems"-View that are correct for the first run of pdflatex and should vanish on the third run.
The hover-test works OK: the hover for a \cite shows the...
2006-11-16 19:17:30 UTC in TeXlipse