It seems that some of the elements on the OOo configuration tree reachable by
API are not updated correctly on the rest of OOo application if changed through API.
To check, follow this sequence on OOo 2.4.1 with en-US user interface, operating
system Debian, en-US user interface on KDE desktop

1) check in Tools > Options – Load/Save – General – “Save†group, the  “Always
create backup copy†checkbox is unchecked.

2) check in Tools > Options – Language Settings – Languages – “Language ofâ€
group, the   “User interface†listbox is set to “Defaultâ€. The two listboxes
“Locale setting†and “Default currency†should be at “Defaultâ€
If not, then set all of them and restart OOo as appropriate.

3) use the following chunk of OOo macro code on 2.4.1 version and run it:

Sub Main
	GlobalScope.BasicLibraries.LoadLibrary("Tools")
	oTheConfigRoot = GetRegistryKeyContent("org.openoffice.Office.Common/", true)
	oTheConfigRoot.Save.Document.CreateBackup = true
	oTheConfigRoot.commitChanges()

	oTheSetupRoot = GetRegistryKeyContent("org.openoffice.Setup/", true)
	oTheSetupRoot.L10N.ooSetupSystemLocale = "it-IT"
	oTheSetupRoot.L10N.ooSetupCurrency = "EUR-it-IT"
	oTheSetupRoot.L10N.DecimalSeparatorAsLocale = true
	oTheSetupRoot.commitChanges()
End Sub

4) now check again the settings:
the one set in 1) above is unchanged, whereas it should have been checked,
the ones set in 2) are correctly changed:
The two listboxes “Locale setting†and “Default currency†are at “Italian
(Italy)†and “EUR € Italian (Itally)†as expected.

If you restart OOo the setting described in 1) above is shown correctly changed
to checked state.
In my opinion after the commitChanges() method returns, the setting described in
1) above should be changed as the other two, without the need to restart OOo.