"Are your daughters in Rome?"
Translation:Suntne filiae tuae Romae?
"Rōmaene sunt fīliae tuae" was marked wrong; however, it seems to me that the word "in Rome" is the one carrying the question, as it were. It's not as though only verbs can be marked with -ne; but you want to put the -ne right away, at the beginning of the sentence (to show your interlocutor that you're asking a question).
I mostly agree, except for two things: I) I don't like the way you use the word "but", since you concatenate two arguments in favour of your position, and II) I'm reasonably certain that it is possible to put the -ne at the end of some word that doesn't occur at the beginning of the sentence in question, since a counter-example may be found here: http://dcc.dickinson.edu/grammar/latin/questions
I checked out your "counterexample", which I guess was the one where mortem and dolōrem (death and pain) are being contrasted.
You're noticing that the word marked with -ne is not the first word of the utterance. Yes.
But, in fact, the quotation does show that 'the word marked with -ne' STARTS the question:
Is tibi mortemne vidētur aut dolōrem timēre? This man, in your eyes, does he seem to fear death, or pain?
I guess Cicero is granting that this man (Is = "he") seems to fear one or the other; and he's interested in "your" (tibi = "in your opinion, in your eyes") take on him. The question is, "DEATH (mortemne) or PAIN (aut dolōrem) ?"
Not a bad illustration, in fact, of how -ne works.
(Notice that the Dickinson commentaries also point out that -ne can be omitted--in which case, presumably, intonation alone carried the question--and this is common when there's a series of questions.)
You would say, in urbe for "in the city," or in oppidō for "in the town," but when you're dealing with the name of a city or town (or small island), you have a replacement for the in + ablative construction: you use the "locative" case, which has died out for most nouns other than the names of cities, towns, small islands (and domus and rūs and a couple of others).
A 1st declension singular place-name (for a city or town: not for a country or continent or region) like Rōma uses what looks like its genitive singular for the "locative" function: Rōmae means "in/at Rome" when it's locative. Similarly with 2nd decl. singular place-names: Brundisiī is locative (for Brundisium ) and Corinthī is locative (for Corinthus ).
(There are different rules for 3rd decl. singular place-names, and for place-names that are plural.)
Don't forget that countries and continents use the in + ablative structure: in Italiā , in Eurōpā , etc.
As the Dickinson grammar site explains, -ne is added to the emphatic word; in that example from Cicero they quote, mortemne is obviously emphatic (Is tibi mortemne vidētur aut dolōrem timēre , "Does he seem to you to be fearing DEATH or pain?"
Normally, as in the many other examples they cite, the -ne will be attached to the first word, since it's not unnatural for that word to be "emphatic" in a question.
We don't have records of actual speech acts, for Latin; we're left to judge on the basis of literary/fictional speech acts (the quote in question is from a dialogue by Cicero, i.e., stylized speech).
I suspect that Duo will want the -ne appended to the first word; also, that Duo will not accept the 'question via rising intonation' without -ne appended at all.
(EDIT). See above for an analysis where the -ne word (mortemne) is the word that starts the question , in any case.