Answer: Based on your description it is impossible to tell whether the problems you have experienced are soil based or something else. Without knowing what the problems are specifically it is hard to make suggestions about what to do to prevent them reoccuring. In the meantime I do not know of any barrier you could use for the raised bed that would prevent contamination by migration since it would probably be carried in the area around the beds as well.
Keeping the soil as healthy as possible is always a good idea, so you might try adding copious amounts of organic matter and especially compost to the beds to try to keep the soil in good shape. Thoroughly cleaning all of your tools and seed starting equipment as well as starting with clean transplants can also help. If you are looking at fungal problems, then making sure there is good air circulation and avoiding wetting the foliage are good places to start at control, as is maintaining a clean layer of mulch to avoid possibly contaminated soil splashing up onto your plants. Always select resistant varieties and also be sure to rotate your plantings; make sure to clean up and remove and destroy any infected plant debris as soon as it occurs and especially at the end of the season.
Finally, you might also want to consult with your county extension about what the problems may actually be and their most up to date control suggestions for them.
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