eclipse java plugin disappears after running eclipse 'check for updates'

I installed eclipse from Software Center. When I tried to add new software, I saw that there were no update site configured for eclipse (its an already reported bug, #873187) .
- After adding the repository for Eclipse indigo, I went to 'Check for updates' .
- After installing all updates that where possible (plataform update was not allowed becase of insufficient priviledges), I restarted eclipse, and JDT plugin was gone (it shows on available updates screen).
- If I remove $HOME/.eclipse , and open eclipse, it appears again.

It seems that updating eclipse through 'Check for updates' messes with eclipse platform. The problem is, otherwise, its necessary to handpick the plugins we want to update to avoid anything installed through apt-get .

ProblemType: Bug
DistroRelease: Ubuntu 12.04
Package: eclipse-platform 3.7.2-1
ProcVersionSignature: Ubuntu 3.2.0-24.37-generic 3.2.14
Uname: Linux 3.2.0-24-generic x86_64
ApportVersion: 2.0.1-0ubuntu7
Architecture: amd64
Date: Wed May 9 10:48:01 2012
InstallationMedia: Ubuntu 11.10 "Oneiric Ocelot" - Release amd64 (20111012)
SourcePackage: eclipse
UpgradeStatus: Upgraded to precise on 2012-01-04 (125 days ago)