Wow! Just found this thread, hope it's not too late to answer your question. First thing; great going on the new growth. Secondly, the root that's above the leaf would be an aerial root til it gets long enough to grow into the media and the leaf eventually falls off. I have a few of those but I'm the type that just let's em do as they please so it's not a big deal to me if it's not in the pot. See:
Most people would have shoved this root back in the pot in the early. If you are having issues with the rotting it may be your environment is more humid and moisture sticks around longer like it does for me. The media you are using may be retaining the moisture a lot longer and if you wet too regular causes the rotting. I switched to the clay balls and coconut husk chunks, it worked. Make sure there is ventilation in the pot to help with the drying out process. Above is one of the 2 orchids I have in plastic pots, the other is an onc, even if you have to make more holes with a hot ice pick (which is what I used to make the plastic container into an orchid pot) or drill or utility knife. Mounting may also be an option, depending on your space available.