I'm using the FindBugs plug-in 2.0.1-dev-20120614-r14386 with Eclipse Indigo SR2 (I also did try the current stable FindBugs plug-in previously). When running the analysis from the Package Explorer, only 6 issues are found. That is far less than what our FindBugs plug-in for Jenkins-CI is finding. I suspected different FindBugs configurations at first, but then it turned out that if I "Open Analysis Results in Editor" I also see way more than 6 issues in the XML file. It seems the XML file is not parsed correctly and the issues are not correctly display in the GUI.
Unfortunately, I'm not able to publicly upload the analysis report here.