Figured I would follow up on this. I had upgraded JunOS and still got the same issue. I pretty much walked away from this whole thing believing that there's just a problem with the hardware on these 400 series phones.
So recently, Mitel released a resolved issue list with the following:
ENG-542554 400 series phones ignore the VLAN assignment in the LLDP policy and sends out DHCP request on native VLAN
So this has been a firmware issue for a long time on these phones. I did some testing and found the phones work correctly about 75% of the time now. So they've made it better, I'm sure they'll continue to improve it.