on two wonder cruises. both times we had no problem. there was a BIG change from the first to the second time as the first trip they only had a retrofitted storage area to accomodate kids...and not many at that!
the second time (this past thanksgiving), the space was completely redone, expanded to about twice its size and very nice. the cms there are wonderful (and typically from the british isles for whatever reason).
of course, our little one is older than yours (he was about 14 months the first trip), but aside from an initial bout of crying with our leaving him (which, i was assured, disappeared about the same time we left), he had no problem. the second night we took him there he basically waved goodbye to us...no tears.
this time (he had just turned 3), we couldn't even get him to wave goodbye! he just ran in, found a new toy (to him, at least) and we were history!!
tip: get to flounders just as quickly as you can upon boarding...they take names and requests for evenings and will let you know the day prior if you have a reservation the next evening. if you are doing the 7-day, i just read that they are open during some of the excursions as well, though i've no experience with that. my advice is request every night and odds are you'll get at least one (we got two on our 3-night cruise and 3 on our 4-night cruise).