Not sure how often this happens and at what time(s) of the year, but when we were there last a couple of years ago around this time of the year we had a problem when a storm blew through... Main storm was done in a day, but left the wind blowing in from the north (i believe) and the seas a bit choppy. The ClubMed boats leave from their dock in grace bay and "could not get out" - for 3 days! On the 3rd day we called Dive Provo and they went out from one of the 2 marinas they use. The seas were smooth as glass on the side of the island we went out!!! We were very happy with sites, the boats, the crew and to be diving! We ended up diving with them the next day as well since we did not want to risk ClubMed not going out. To the credit of the folks running the dive op at ClubMed they refunded us for all the dives we did not do with them even though they did manage to go out the last day. So if you are looking to do the ClubMed thing with a little diving on the side then use their inhouse op, otherwise pick one of the dive ops and really get excellent sites and no cattle boats.
Here's a tip if you are staying at ClubMed and diving with another op, there may be an hour time difference from the resort and the rest of the island!!