Java’s default heap size (at least last time I researched it) is 128 MB. The latest version of Eclipse (i.e. Helios) is set to run with a default heap size of 512 MB. (see the eclipse.ini file in your Eclipse base path).
Therefore, you are probably seeing this behavior because your application needs a heap size greater than 128 MB… which it doesn’t get from your system JVM’s defaults, but DOES get within the Eclipse JVM process.
In your Web Start “.jnlp” file, look for the first <j2se> element, and add a max-heap-size attribute like this:
<j2se version="1.3" initial-heap-size="256m" max-heap-size="512m"/>
Reference
http://download.oracle.com/javase/1.5.0/docs/guide/javaws/developersguide/syntax.html