I am successfully deploying .ears under JBoss-IDE/JBoss 4.0.0 combination. Without knowing specifics, it's hard to provide you with any helpful feedback.
However, I did have one area of difficulty you might want to look into. Sometimes, I found that relatively simple bugs in my code caused the JBoss server running inside Eclipse to crash. When I restarted, I started getting .ear deployment problems, although I also had these when running from a shell.
The resolution was to look in server//deploy/tmp. There I found directories representing partially-exploded ear files, which resulted from failed deployments.
Shutting down Eclipse, removing the .ear from the deploy directory, removing these partially-exploded directory structures and restarting was sufficient to return me to a clean, stable state.
Hope this helps,