Changing default thumbnail size in user preferences should change image size on the page. It does happen in page preview, but it does not happen on the page itself. The image size on the page can no longer be controlled via user preferences.
This issue appeared in Russian Wikivoyage yesterday (16.04), and it seems to be generic across different projects. Note that it does not appear until page cache is purged.
Concrete example:
https://ru.wikivoyage.org/wiki/Лодзь
Here, all images are supplied with the upright= parameter to allow image size control via user preferences. However, it does not work.