I've found that items that show up at the end of a romlist out of alphabetical order, is caused by having it begin with a lowercase letter. I don't know why it does this, but if you rename the item with a capital and rescan, they will end up back in order. Check and see if the rom starts with a lowercase letter, and if it does, that is the problem. In your case, it is because those systems you listed (naomi), (model2) are in lowercase, and (MAME) is not, changing them to(Naomi) and (Model2) with capitals will fix that.