I was getting frustrated that my plants wouldnt grow, so I dug out a couple seeds and moved them so that the sprouts(1cm long) just stuck out of the ground. Was that too much for the plant to handle?
your not talking about the tap root are you? the tap root should be facing down, emmerised in the soil. The sprouts should be fine, make sure the light isn't too intense. are you using CFL, MH, or HPS? CFL can be much closer than the latter two. When you transplant later on, you can re bury then up to the cotyledons. (two circle leaves that eventually fall off)
sorry forgot, something else you should keep in mind through out this entire process. It is going to take a lot of time. let that sink in. You need to be patient with your plants. In all proboblility, the longer it all takes, the better the bud, and the more of it you will have. Peace