Speculation
I'm "Guardian" level contributor to EFF which gets me a newsletter (free on their website) and various tschotskes if I want them. But I am as much in the dark as everyone else.
I can think of two possibly controversial recent actions that Williams may have disagreed with - EFF's support of Assange and their support of the Palestinian digital rights group 7amleh. I frankly can't see Williams objecting to either.
But, I can think of one of Williams' positions that the EFF might have a problem with - his growing identification with drug law reform and marijuana legalization.
I suspect it was the latter and the EFF wanted to distance itself from these issues (and the whole 'encryption helps drug gangs' narrative) but retain Williams as an advisor.