Thanks for the suggestion. I'm listening to some live concerts so audible gaps amid crowd noise between tracks is obvious. The gaps don't show up when I play FLAC on PC or even mp3 on the X3.
My qaac commandline is just: "-V110 --silent - -o %d"
I suppose I could re-encode my FLAC to mp3, but I'd rather not bother.
Do I need to be a beta tester to use the beta firmware? I never signed up for that. What do you mean by resetting the X3? Just the hard reset with a paperclip/whatever?
Yes. Hard reset with a paperclip on the button up top. No, you don't need to be a beta tester for the beta. Click http://www.head-fi.org/t/725256/fiio-x3-beta-firmware-3-00ex-available-for-download-added-beta-exfat-support, and download the beta. Load it on a card, update your X3's firmware, and try again.
I think your problem might be the qaac. I have my library in plain old aac. Maybe re-encode?