At Ibiza last week I was (on arrival) directed to the EES register machines (I was previously registered in May) which rejected me - got the big red cross with "proceed to control" underneath - which, of course, I could have done in the first place if the officials had listened!
Anyhow, at the e-gates, the first one failed, the second one failed, and I got through the third time - so there's either a fault with my passport/initial registration or those e-gates themselves. Took under 5 mins though.
On return at Ibiza the passport was just scanned prior to the gate, only issue is once through the e-gate it gets very crowded between the gate and the desk if they haven't started boarding.
That was exactly my experience there when I went the other week.