Answer: I would strongly suggest you run some soil tests and check fertility levels as well as the pH. Compost can have varying qualities depending on what ingredients went into it and how it was handled and stored, so it is possible there are some basic nutrients lacking.
It also possible the pH may have drifted over the years to a point where it is no longer optimal for tomatoes. (Peppers are closely related to tomatoes so they have similar needs.) Testing is the only way to find out.
Your mulch material might also be tying up nitrogen, if it is very woody.
If you have rototilled repeatedly, there is a possibility you have created a hardpan under the garden area and this prevents them from rooting the way they should. To counter that you might try growing a deep rooted cover crop such as buckwheat, and/or you could double dig the area if it is not too large.
Keep in mind also that it is important to rotate your crops to not only avoid disease or pest build up but also to allow the soil time to recover from the depletion caused by certain crops. Depending on your rotation, you may inadvertently be planting into fairly depleted soil. Planting them immediately after a heavy feeder such as corn, for example, could have an adverse effect.
Make sure if you are using any weed preventer chemicals or herbicides that you are following all of the label directions exactly and if these are being used in nearby lawn area make sure there is no accidental overspray onto the garden area.
Finally, make sure you are planting good quality transplants that have been well cared for; they should not be pot bound, they need to be hardened off before planting, and they should not be planted until well after the last frost when the soil has had time to warm up. Planting into cold soil or exposing them to temperatures below 45 degrees can stunt the plants.
I hope this helps you troubleshoot.
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