Whatever is going on has nothing to do with the dark spots on the stems which is normal.

that is a relief that the black spots is normal. But the jalapenos in particular seem covered with blackness/leaf spots. they look very unhealthy. Even some of the jalapenos that were started from the same batch -- I had given to my mother and hers look very healthy with not special attention - she just put them in the ground.. Am I doing something wrong?

The black color on the stem at the leaf joints is normal. The spots on the LEAVES are NOT normal.

Sorry, but I don't know what it is or what caused it.

This is an extremely late reply, but for anyone here who has the same question, the black spots on the stems are normal and occur in early spring. However, if there are black spots on leaves, they need to be treated urgently and can spread very easily if left untreated. If you do have black spots on your leaves, watch this video on how to treat them:

https://www.youtube.com/watch?v=xwlbK0gZkPw