We've had similar experiences both on liveaboards and land-based trips. We work crazy long hours before leaving town and stay up all night to pack. Then the air travel causes a lot of congestion and exposure to colds and we are susceptible because we are physically run down. So we have spent time at resorts and on liveaboard with colds and ear infections and unable to dive and it is a real bummer.
I think the worst was our trip to St. Croix several years ago. We both came down with colds while we were on the liveaboard and then my husband got an ear infection and we were unable to dive for the last part of the trip. When we got off the boat to spend a week on the island my cold turned into bronchitis and so we still couldn't dive or do as much as we wanted to do.
After that we made some changes. Somehow we still can't seem to avoid working long hours and losing sleep and arriving exhausted - but now we build some cushion time into the beginning of the trip to relax, sleep, and get over the jet lag and sinus congestion. We no longer arrive and immediately rush out to catch the afternoon dive boat or jump on the liveaboard to begin a cruise. We give ourselves some time to rest and get healthy. It's actually nice and a lot of fun!
We also take Allegra D 12 hour each dive day to clear the sinuses. There is a lot of debate about the pros and cons of taking anti-histamines and decongestants before diving and I don't know how you will react to such drugs but it has worked well for us. You should probably try it at home to see how your react.
Finally, and this may seem goofy, but we use netipot rinses every vacation night to clean our sinuses. My ENT doctor kept recommending the netipot but I was a slow believer, but after the St. Croix trip I decided to give it a try. It is not difficult, you add a pre-measured salt packet and fill the pot with distilled water to the line, then gently warm it in the microwave and pour the salt water slowly through your nostrils and it clears a lot of nasty gunk out of your sinuses and makes it harder for germs to breed.
When you are in a resort or on a liveaboard this isn't always easy to do, but I mix the salt with water from a new bottle of drinking water and then set it in the sink in a couple of inches of warm water until it reaches a comfortable warm temperature. My husband was even slower to adapt this process but when he saw me having success he became a believer. And why not give it a try? It is cheap, painless, easy, drug-free, and I really believe it helps.
Even at home when I feel a cold coming on I start using the netipot to avoid or shorten the cold. It doesn't hurt and I think it is beneficial. And it is better than letting a cold ruin your expensive and long-awaited dive vacation IMO.
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Another motivation is whether or not my GF can exchange one of her time-shares at a location where there is good diving that our airline flies too (that would be the airline that we have a bunch of miles and a companion pass with). When we went to Hawai'i in March that was driven by the $335 RT airfare offer I received in my email. I figure sooner or later I'll get to many of the places I have on my mental list. Meanwhile, they are all good!!! 
