Additional debugging tips (thanks Nikerabbit):
1) There is specific debug log for translation services: $wgDebugLogGroups['translationservices'] = 'file', 2) Use the browser's developer console to inspect the AJAX requests to see if it contains explicit error message for MT section.
Federico Leva (Nemo), 22/03/2016 09:45:
Hi Andrew, sorry for seeing your question only now. What Apertium configuration are you using exactly? Can you detect any pattern in the units which don't show the translation suggestion? For instance, are they longer, or do they contain a lot of non-alphanumeric text? If it seems completely random, did you enable debugging and do you see any error in the MediaWiki or server logs? I'm trying to understand whether your issue could be with performance or some kind of intermittent networking issue (as happened in the past).
Nemo