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