Sorry I didn't reply back to this...I tried doing the tree a different way which worked but suffered from severe performance issues, so I'm back to trying this.

Relevant code from ProgramTaxonomyAction

public Set<Taxonomy> getTaxonomies() {
 Program program = programService.getProgramByID(userBean.getCurrentProgram());
 taxonomyBean.setMode(ProgramTaxonomyBean.DISPLAY_MODE);
 return program.getTaxonomiesByType(taxonomyBean.getTaxonomyCategory());
 }

package org.act.vsl.beans.metadata.classification;

import java.util.HashSet;
import java.util.Set;

import org.act.vsl.beans.Program;
import org.act.vsl.beans.VSLObjectImpl;

public abstract class TaxonomyImpl extends VSLObjectImpl implements Taxonomy {
 private String code;
 private String description;
 private Taxonomy parent;
 private Set<Taxonomy> childTaxonomies;
 private Program program;
 private boolean isOrganize;

 public TaxonomyImpl() {
 }

 public void setCode(String code) {
 this.code = code;
 }

 public String getCode() {
 return code;
 }

 public void setDescription(String description) {
 this.description = description;
 }

 public String getDescription() {
 return description;
 }

 public void setParent(Taxonomy parent) {
 this.parent = parent;
 }

 public Taxonomy getParent() {
 return parent;
 }

 public void setChildTaxonomies(Set<Taxonomy> childTaxonomies) {
 this.childTaxonomies = childTaxonomies;
 }

 public Set<Taxonomy> getChildTaxonomies() {
 if (childTaxonomies == null) {
 childTaxonomies = new HashSet<Taxonomy>();
 }
 return childTaxonomies;
 }

 public void setProgram(Program program) {
 this.program = program;
 }

 public Program getProgram() {
 return this.program;
 }

 public void setIsOrganize(boolean isOrganize) {
 this.isOrganize = isOrganize;
 }
 public boolean getIsOrganize() {
 return isOrganize;
 }
}

Is there any chance that the child nodes being lazy loaded by hibernate could be the problem? I don't see HOW it could be the problem, but it is the only thing I can think of.

Apparently that isn't it either. I turned off lazy loading of the taxonomy children and tested with a smaller tree and it still would not go any deeper.

The tree I tested it with has a very simple structure:
Content 1-1
|- Content 1-2
|- Content 1-3
|- Content 1-4
|- Content 1-5

It will display content 1-1 fine, but then displays content 1-2 as a leaf node.

Apparently this had something to do with the server I was using. This problem happens when I run the application through JDeveloper, but when I deploy the app to a regular OC4J container it works normally.