brown spots on seedling leaves

so i built a new dwc bubbler for my seedlings, and it took a little longer than i thought and i had to hand water the rockwool cubes of 2 little guys i just sprouted, anyways after i got them in the bubbler they started getting tiny brown spots on the leaves which apparently lead to the leaves dying, the seedlings are still very young (2 pairs of true leaves) and are still producing roots and new growth - im just wondering if its the new setup somehow or just the fact that they were stressed because i didnt get them in a proper medium right away. im gonna keep trying to get them going, and i put a new one in as a control-type-deal to see if the same thing happens to it, but id love some input if you guys have any ideas. ill try to get some pics up later, if i can find my camera. also lighting isnt the issue im using the same cfl setup ive used countless times successfully.