Silva, all mine go in 1/2in deep and I have not had any issues. The key is moisture control. Look at your seed starter mix in dry state, a light brown shade of some source. Now water the tray up real well. You see moisture on top, almost as heavy as if you sprayed the top? You don't want that. You are looking for right in the middle of those two shades, light brown and dark brown almost black. Feel the weight of the tray both dry and soaked and look for half way again. If you can keep this consistant you will need no dome over your trays. I have never used the dome and I get plenty of babies to pop!
It sounds like you are getting on top of the issues. Just try and replicate what the situation has been the last week. You are getting babies so it's working in your favor. Good luck!