In most modern IDEs there is a parameter that you can set to ensure javac gets enough heap memory to do its compilation. For reasons that are not worth going into here, we are tied for the time being to JBuilder 2005/2006, and it appears the amount of source code has exceeded what can be handled by javac.
Please keep the answer specific to JBuilder 2005/2006 javac (we cannot migrate away right now, and the Borland Make compiler does not correctly support Java 1.6)
I realize how and what parameters should be passed to javac, the problem is the IDE doesn't seem to allow these to be set anywhere. A lot of configuration is hidden down in the Jbuilder Install\bin*.config files, I feel the answer may be in there somewhere, but have not found it.