I have a very vague recollection we faced something similar to this, and dealt with it by (massively) increasing the EAPOL timeout on our wireless controllers.
IIRC the problem is that you have to hit "accept" fast enough that the original EAP conversation is still in-play. This is a function of both FreeRadius (timeout of EAP conversations) as well as your wireless platform.
But I might be mistaken - it's a very hazy recollection.
I dont have a straight EAPOL timeout option on my controller (Enterasys HiPath C4110), so I set the Radius timeout to its max - 360 seconds. It still fails....and does so fairly quickly. I tried putting on v2.1.10 and it still fails. I get this error: WARNING: !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! WARNING: !! EAP session for state 0x918d31e1948b2881 did not finish! WARNING: !! Please read http://wiki.freeradius.org/Certificate_Compatibility WARNING: !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! But I think it may be a bit of a generic error as Im using a total default config, including the certs that were generated with the bootstrap script.