The reason is because the timezone select is defined in the Admin Application, as a custom display of the XWikiPreferences#timezone field (This is bad... Custom displays should be left to users.)
When on an empty wiki, i.e. without the Admin app, the XWikiPreferences class is created from java in oldcore and doesn't have the custom display for the timezone.
Solution 1: Modify the Java generation of XWikiPreferences to contain the custom display code in Java too.
Solution 2 (best): Create a new Timezone class property type and a displayer.