First about your plugins.
When you say that you see plugins, it looks like you see physical folders and banks. The best way is to use the dialog box: help => about eclipse => installation details
There are a number of informational tabs that will tell you what your configuration consists of. Including the last tab showing the eclipse initialization log.
Then you can also view the log using its highlighted view: window => show view => error log.
In general, the problem, as you describe it, seems to be related to permissions. Either in the eclipse itself, or in your workspace, or in Java itself. First I would check it out!
Now about the remote cause of your difficulties.
It seems you installed eclipse via apt. It's not obligatory.
- apt versions are always late for stable eclipse releases.
- You do not learn plugins when an update is applied to you.
The reason Debian people use apt is because it takes care of all the dependencies. However, an eclipse has very few external dependencies: the JRE and all and many internal dependencies. This is why you have pre-packaged eclipse packages.
In addition, using apt can lead to an unwanted update of the eclipse during your installation, when you need it less. This is what happened to you.
In the future, if you want to stay on the safe side, do not use apt, go to the eclipse download page and grab the latest stable version. It is enough to remove eclipse, although synaptic, and then reinstall the downloaded version and then reinstall your plugins. So when Natty arrives after 2 months, you no longer have to repeat everything.