Joey,
I've had the pleasure (or misfortune) of working with dozens if not hundreds of "pop artists". While most people on this board seem to disagree with your methods I have to say that what you're doing is totally right and necessary. I tune and time every word/syllable all the time.
Melodyne does have bad sync issues sometimes, but mostly it's do to buffer settings IN CUBASE...change your settings there to less CPU intensive and melodyne will run better. I always tune first/time later, as that way the melodyne "slippage" is compensated for later.
I also use protools EA audio for vocals. Lead vocals I try to avoid it, but if you don't have Vocalign, it's the easiest way to layer and time Bg vox together. Doesn't Cubase have elastic audio as well? or something similar?