Mud and water at base of sapling tree

We have escaped the storms this month relatively unscathed, but parts of the ground are becoming waterlogged with the persistent rain.  In the first storm a branch came down from one of our trees and today we had to take emergency action to clear standing water from around the bases of our newly planted fruit tree saplings. In the greenhouse the autumn sown peas and broad beans are thriving and the latest sowing, which also included sweet peas, have all germinated. The winter gem lettuce is still struggling and the spring onions look sorry for themselves. Indoors the window sills are filling up with seedlings: tomatoes, aubergines, cabbages, cauliflower, broccoli, leeks and cabbage together with assorted flowers. Some are in warm rooms, others cooler. I swapped to peat free compost and am struggling to gauge the watering, especially in the propagator where the surface quickly dries out under the heat from the lights. After four weeks still not sign of the Trinidad chillis germinating. Have I killed them or am I being impatient?