Badflash made a good point...maybe they are too wet.
My buddy had hot peppers growing in media beds on timers. His seemed to do pretty well (untill some other plants started to shade them too much)
I don't think they got as wet, as in a media bed with a bell siphon set up.

The other thing to think about...how mature are your systems ? Peppers and tomatoes seem to do better in a very mature sysytem, especially the peppers.

You might try spraying them everyday, or every other day, with some maxi crop and molasses. Worth a try, It might help..."?'