Well, a little bit more information on how to reproduce this bug would be nice. :)

it actually should be enough to build the current release tag
and then check if its there,

possibly changing some code building again and check if its there.

maybe (this is more a feeling), it occurs if you ONLY change resources and no source code, and the build again.

This bug could not be fixed during the 2015.05 release.
Setting target_milestone to AfterNextRelease

The offending code seems to be in
void QmitkPreferencesDialog::UpdateTree()

the lines
if(it->treeWidgetItem == nullptr)
{

if(it->category.isEmpty())
{
  it->treeWidgetItem = new QTreeWidgetItem(d->m_PreferencesTree);
}
else
{
  it->treeWidgetItem = new QTreeWidgetItem(items[it->category]);
}

}

items[it->category] returns a nullptr if a child item is parsed before a parent item. The parsing order seems to be random.

User goch has pushed new remote branch:

bug-19097-fix-incomplete-preferences-list

[404d74]: Merge branch 'bug-19097-fix-incomplete-preferences-list'

Merged commits:

2015-08-19 11:50:30 Caspar Goch [495942]
Added missing reference

2015-08-18 19:22:43 Caspar Goch [0befb3]
Defer preference page addition if it is not a top-level preference page