The 'scan frequency' (press and hold the left or right button) feature isn't working in the tuner for me.
Other than that, all systems go so far. Seeking and track-switching for FLACs seems to be much improved, and I can finally seek cleanly in Ogg Vorbis files.
Still not as fast as MP3, but acceptable.

I also had some problems with the post-upload stages (rebuild, reboot, etc.) of jEmplode, but not much worse than usual, so that might just be a coincidence: only about one sync in five is error free for me in jEmplode, on either of my empeg units.

Single HDD, Hijack v435 with ext3 filesystem.