I have just noticed that one of multilingual sites we are managing has a completely different set of sitelinks depending on whether the site is shown on google.com, google.de, google.it or google.hr. Not just different pages and different anchors are shown as sitelinks, but there is also a different number of sitelinks shown when the site is displayed in search results on each of above mentioned google domains.
Webmaster tools shows only one set of sitelinks, the one that appears on google.com (english). The other three sets of sitelinks are not shown in WMT and therefore there is no way of managing them.
The site also runs in two more languages, but sitelinks on these google domains show english sitelinks. However, these remaining two languages do not have as much traffic as the above mentioned four.
Interestingly, the domain itself is ccTLD domain with the home page in english, but as it is ccTLD there is no way to set up geotargeting on a folder level. However, the domain uses folder structure for all languages other than english.