Take a read through this if you have not already:
I am getting convinced there is an issue with the 2000 AP hardware, firmware 3.5, Netonix switches when the AP has STP turned on. I have three 2000 APs and all three of them I lost control of on the Ethernet side when I tried to upgrade to 3.5. All three are in Netonix switches and all three use STP. As a result, I have not upgraded those APs.