Hello simon,
I finally had some time to do some searching. It sounds like something like blossom end rot that's common in tomatoes, but I wanted to find out if squash and zucchini were susceptible to it as well. Because you have the same problem in both soil and hydro, I would say it has more to do with the environment than the method.
First I know squash has both male and female flowers, and only the female ones grow fruit. But They also need to be pollinated properly, and unlike some plants like tomatoes that can be pollinate with air currents, squash needs insects to transport the pollen from flower to flower. I know they can be hand pollinated if you know witch is the male and female flowers. You may try to hand pollinate for a while to see if you get better results. With tomatoes blossom end rot (BER) can be related to uneven watering, or drying wind. I don't know if those conditions exist for you or not, but may be some things to consider. I know Florida is generally humid (and/or rainy) and that can play a part, and affect proper pollination as well. I would also look for insects as a source of a problem. They can transmit viruses as well (soil or hydro), particularly aphids. Look closely at the undersides of the leaves, as well an any new growth, that's where they attack first. Especially ones that affect good pollination, diseases,viruses, then calcium uptake.
Here are a few quotes and links I found:
Ask the ISU Garden Experts About: Zucchini Rot, Grass Spiders and Iris Borers
"The fruit on my zucchini squash began to grow, but quickly turned brown and rotted. Why?
The rotting of the small squash fruits could be due to poor pollination or blossom-end rot.
For squash fruit to develop fully, bees and other pollinators must transport pollen from the male flowers to the female flowers. If the female flowers aren’t pollinated properly, the fruit will begin to grow and then suddenly shrivel up and die. The rainy weather could be responsible for poor pollination and rotting of the small fruits because bees and other pollinators are less active in rainy weather. Drier weather conditions should increase pollinator activity."
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HGIC 1321 Summer Squash : Extension : Clemson University : South Carolina
"Problems
Insect problems include spotted cucumber beetles, striped cucumber beetles, pickleworms, squash vine borers, aphids and squash bugs. Aphids are a major problem because they can transmit viruses to the plants. Squash vine borers can cause total collapse of the plant. Plant early because squash vine borers and pickleworms are problems later in the season. Common disease problems include powdery mildew and viruses."
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AZ Master Gardener Manual: Squash
"Diseases........Powdery and downy mildews, blossom blight, bacterial wilt, virus.
Insects.......Cucumber beetles, squash vine borers, whitefly, aphids, leaf miner.
Cultural.......Blossom end rot from irregular moisture or calcium deficiency; flower drop may occur normally when female flowers form before male flowers or during periods of heavy fruit set."
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Fruit Rots of Squash & Pumpkins fact sheet Control of Squash and Pumpkin Rots (near the bottom of the page)
Disease Fact Sheets Listed by Crop
Diseases (right hand side on page 3)
Questions on: Squash
U of M Gardening Information: What's wrong with my plant?
Produce Quality and Safety (Virus/Diseases about the middle of the page)
Squash
http://santarosa.ifas.ufl.edu/docume...ollination.pdf (pictures of male and female squash flowers)
Techniques for hand pollinating squashes (page 2)
P.S. Calcium deficiency is a cause of blossom end rot. But lack of calcium is often not the problem, calcium uptake/deficiency are usually related to environmental conditions, thus the plants ability to take up the available calcium, rather than a lack of calcium (soil or hydro). But especially in hydro when using balance, pre-manufactured
nutrient solutions, that are manufactured balanced in the first place. Unlike in hydro, soil is difficult control the balance of
nutrients. With the same issue in both soil and hydro, I would be looking at environmental issues first. Especially ones that affect good pollination, diseases/viruses, then calcium uptake.