Sorry, upload of the log file is not working, but here is a snippet. This is the only message if I open, change and 
close the "Global QNX Preferences" dialog:

!ENTRY org.eclipse.jface 4 2 2010-04-22 07:41:48.550
!MESSAGE Problems occurred when invoking code from plug-in: "org.eclipse.jface".
!STACK 0
java.lang.NullPointerException
	at com.qnx.tools.utils.QnxConfig.initFromEnvVars(Unknown Source)
	at com.qnx.tools.ide.ui.GlobalPreferencePage.createContents(Unknown Source)
	at org.eclipse.jface.preference.PreferencePage.createControl(PreferencePage.java:232)
	at org.eclipse.jface.preference.PreferenceDialog.createPageControl(PreferenceDialog.java:1501)
	at org.eclipse.jface.preference.PreferenceDialog$14.run(PreferenceDialog.java:1258)
	at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
	at org.eclipse.core.runtime.Platform.run(Platform.java:888)
	at org.eclipse.ui.internal.JFaceUtil$1.run(JFaceUtil.java:48)
	at org.eclipse.jface.util.SafeRunnable.run(SafeRunnable.java:175)
	at org.eclipse.jface.preference.PreferenceDialog.showPage(PreferenceDialog.java:1252)
	at org.eclipse.ui.internal.dialogs.FilteredPreferenceDialog.showPage(FilteredPreferenceDialog.java:679)
	at org.eclipse.jface.preference.PreferenceDialog$10.run(PreferenceDialog.java:708)
	at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70)
	at org.eclipse.jface.preference.PreferenceDialog$9.selectionChanged(PreferenceDialog.java:704)
	at org.eclipse.jface.viewers.StructuredViewer$3.run(StructuredViewer.java:864)
	at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
	at org.eclipse.core.runtime.Platform.run(Platform.java:888)
	at org.eclipse.ui.internal.JFaceUtil$1.run(JFaceUtil.java:48)
	at org.eclipse.jface.util.SafeRunnable.run(SafeRunnable.java:175)
	at org.eclipse.jface.viewers.StructuredViewer.firePostSelectionChanged(StructuredViewer.java:862)
	at org.eclipse.jface.viewers.StructuredViewer.handlePostSelect(StructuredViewer.java:1175)
	at org.eclipse.jface.viewers.StructuredViewer$5.widgetSelected(StructuredViewer.java:1200)
	at org.eclipse.jface.util.OpenStrategy.firePostSelectionEvent(OpenStrategy.java:251)
	at org.eclipse.jface.util.OpenStrategy.access$5(OpenStrategy.java:245)
	at org.eclipse.jface.util.OpenStrategy$3.run(OpenStrategy.java:419)
	at org.eclipse.swt.widgets.RunnableLock.run(RunnableLock.java:35)
	at org.eclipse.swt.widgets.Synchronizer.runAsyncMessages(Synchronizer.java:134)
	at org.eclipse.swt.widgets.Display.runAsyncMessages(Display.java:3885)
	at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3506)
	at org.eclipse.jface.window.Window.runEventLoop(Window.java:825)
	at org.eclipse.jface.window.Window.open(Window.java:801)
	at org.eclipse.ui.internal.dialogs.WorkbenchPreferenceDialog.open(WorkbenchPreferenceDialog.java:211)
	at org.eclipse.ui.internal.OpenPreferencesAction.run(OpenPreferencesAction.java:65)
	at org.eclipse.jface.action.Action.runWithEvent(Action.java:498)
	at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:584)
	at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:501)
	at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionContributionItem.java:411)
	at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
	at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1003)
	at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:3910)
	at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3503)
	at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:2405)
	at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2369)
	at org.eclipse.ui.internal.Workbench.access$4(Workbench.java:2221)
	at org.eclipse.ui.internal.Workbench$5.run(Workbench.java:500)
	at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
	at...

The configuration path is:
QNX_CONFIGURATION=C:\Program Files\QNX Software Systems

And I can select my configuration xml file in the IDE 4.7:
C:\Program Files\QNX Software Systems\qconfig\qnx_6.4.1.xml

The values from the xml file are displayed correct after selecting it in the dialog "Global QNX Preferences":

Install Selection
Select Install: "QNX 6.4.1"
Version: "6.4.1"
QNX_HOST Path: "D:/P4SPOT/deliveries/m641/bin/sys/qnx/host/win32/x86"
QNX_TARGET Path: "D:/P4SPOT/deliveries/m641/bin/sys/qnx/target/qnx6"

The "qnx_6.4.1.xml" is working with IDE 4.6.1. The "QNX_CONFIGURATION" variable is the same for both IDEs. 

A difference between IDE4.6.1 and IDE4.7 in the "Global QNX Preferences" dialog: In the IDE4.7 I can not see the buttons
 "Restore Defaults" and "Apply". I just confirm with the "OK" button.