In Mandarin should there be any difference between the pronounciation of the pinyin final in "jiu" and the pronunciation of the pinyin whole word "you"?
The pinyin Final "iu" contains a hidden "o", so it is pronounced "iou".
"y" is actually an "i" Final being used as an Initial.
So the answer is: if both are the same tones, no :)
Same tones as in: 就 (jiù) and 又 (yòu)