Did the books ever address the language issue? After all, people didn't speak English at many places that Jack and Annie went to but they're able to communicate with everyone just fine. Is it part of the magic (like the way their clothes change)?
That's probably the case. Either that, or it's meant to be an Acceptable Break from Reality, of which there are a lot (I mean, language aside, two white American kids strolling around with no adult supervision is definitely going to raise eyebrows in a lot of places/time periods).
Why are Jack and Annie so surprised to be in the present but in a different place in Eve of the Emperor Penguin when lots of the early books focused on them visiting other places (Africa, the Amazon, Australia) rather than other times? In Dolphins at Daybreak it was almost explicit that they didn't travel through time given that Jack identified the dates in the minisub's log as beginning "last week" and going on for several days.
Eve of the Emperor Penguin was notable for being the first book in which Jack and Annie actually encounter other people in the 21st century. The earlier books that involved traveling through space, but not necessarily time did not include anyone who would question or worry why two kids are wandering around by themselves, so that was probably very jarring for them.