I **stumbled** on this by accident (short/long story about disabling swap and reusing that partition to try to install XP and flash firmware)
When I was using my Echo AF12 initially it worked flawlessly (and I had no swap partition enabled) ... solid for 20 minutes at 3x64 and 48kHz -- even storing WAVs to external USB2 HD.
At some point after that I wiped the XP partition (never used it for updating firmware, brought AF12 to work and [ab]-used an XP+SP2 machine there) and re-enabled swap at boot (/etc/fstab)
and I was getting XRUNS regardless of what jackd settings used with ffado. Just COULDN'T stop them, and I was smart to remember the change I did and reversed it (swapoff /dev/sdX) and restarted and tada SOLID
so a work around for those having XRUNs and for testing purposes is to disable swap memory (can script it inside qjackctl via gksudo swapoff /dev/sdX)
I have a sneaky suspicion that some buffer and/or code space (perhaps all of it) isn't properly "locking" it's memory or something like that. Since I don't fully understand the details... I'll shut-up and leave it at that.