First about your plugins.
When you say you "see" the plugins it looks like you see the physical folders and jars. The best way is actually to use the dialogue box : help => about eclipse => installation details
There are a number of informative tabs that tell you what your configuration is actually made of. Including the last tab showing the log of the eclipse initialisation.
Then you can also see the log using its dedicated view : window => show view => error log.
Overall the problem as you describe it seems to have to do with permissions. Either in eclipse itself or your workspace or java itself. I'd check that first !
Now about the remote reason for your predicaments.
You seem to have installed eclipse through apt. This is not necessary.
- apt versions are always late over stable eclipse releases.
- You don't master plugins when an upgrade is inflicted on you.
The reason why Debian folks use apt is because it takes care of all dependencies. However, eclipse comes with very little external dependencies: the JRE and that's all and a lot of internal dependencies. This is why you now have pre-packaged eclipse bundles.
In addition, using apt may force an unwanted eclipse update on your installation when you less need it. This is what happened to you.
In the future, if you want to stay on the safe side, don't use apt, go to the eclipse download page and grab the latest stable version. It's sufficient to uninstall eclipse though synaptic and then reinstall the downloaded version and then reinstall your plugins. So that when Natty comes in 2 months time, you don't have to redo everything again.