In most contexts, putting the stress on did in OP's construction effectively uses that word as a "proxy" for stressing the word where - which would normally imply the speaker is genuinely and intensely interested in knowing where the other person came from. But...
Unless delivered in some (contrived) context where there's no obvious entrance through which the other person could have (just) appeared, it's far more likely to be a rhetorical question. That's not to imply the asker already knows the answer - he probably neither knows nor cares. He's just obliquely referencing wherever you came from scornfully. Probably implying something like....
"They don't teach very good manners wherever you came from"
...or some other snide put-down of your place of origin (effectively, of you).