1/provide a full reproducible testcase so a bug can be logged and the issue can be worked in Oracle using the source code. Not sure about 4.0EA but if it happens with production SQLDeveloper and production database - you can go through official Oracle support.
2/Do not install SQLDeveloper 4.0 EA1 on top of another SQLDeveloper installation
3/Use latest Java7
4/Are you using multibyte characters? (Chinese or Japanese being the most widely used in support calls)
5/Try as a operating system different user
In case your preferences are corrupt. (you can move your existing preferences out of the way - but using another user seems to avoid any support/user error possibilities.)
6/Try with SQLDeveloper 3.2.2
7/Try with SQLPLUS
Most serious java issues cause a message to the screen ('Java Stack Trace') if you start sqldeveloper from ide/sqldeveloper/bin from the command line
There is also View->log->Logging Pane - which probably gives too much information
[This blog has an introduction to tracing http://totierne.blogspot.co.uk/2013/02/introduction-to-tracing.html entry for the more adventurous - there is lots of information but the important bit is you can see exactly what is being sent to and from the database.]
9/Try the query as run statement, run script, try count (*), try a subset of columns, try to_char() the columns so the data transformation is mostly done in the Oracle Database
10/Are you using thick(i.e.OCI) or thin jdbc connection type? What driver are you using? What database are you using(try 'show jdbc' worksheet command) Is tools-->preferences->database->advanced->Use OCI/Thick driver checked
11/If trying with sys - try as another user.
12/When installing run as the installing user once so the JDK version can be put in the configuration file.
13/Useful SQLPLUS emulation features:
set echo on
set verify on