Static-like digital "pops" on CDs - can be what?

For your second question, Onkyo pre/pros are bad about taking a sec or so to lock into the audio stream. It drove me so crazy I got rid of mine. Some have a "lip synch" setting, so check for that to see if you can adjust the synch of audio. I have a Pio now and it works with no issues. ARe you using HDMI?

You might also be possibly hearing some audible artifacts from cd "rot." I've experienced this on some older classical cds I've had since the eighties. I've ripped them to iTunes using error correction and the copied discs all play flawlessly. You might try ripping a disc in question and see if the copy share the same anomalies. Then you'll know if it's software or hardware issues.

Clicks and pops can be caused by a dirty disk (I remember attending a Sony introductory demonstration is San Diego when CDs first came out. A "click" clearly happened and the audience jumped all-over the MC who could not explain it).

I have noticed something that sounds like a "snag" when playing SACDs on the new Sony 5400ES.
It doesn't happen often but it does happen.

Hmm. I was thinking of ripping a couple CDs where it happens to send with the unit whenever I try to get it repaired. I didn't think to actually try the ripped versions first, so I will do that and see if the same clicks happen.

I don't think it's that the discs are dirty, since they didn't have any clicks and pops with my Sony player (which I can plug in and verify that it doesn't happen), they are newish discs, and it always is just longer discs and towards the end of the longer discs when it happens.

My Integra pre-pro is unfortunately pre HDMI (not that I care about sending audio over HDMI, but it would be nice on the video end to have switching built in), so I am not sending audio that way. I'm using coax digital connection. I did not have any timing issues with the Sony player at all, nor with my Oppo. I tried messing with the sync adjustment on the Integra player itself, but that didn't seem to affect the CD playback.

I'm glad to hear someone had the same issue with this player - I'm guessing that is where the problem lies.

How do you like your 5400ES? Heard a lot of great things about that player, unfortunately the lack of multichannel outs is a dealbreaker for me.

Right now I'm using the 5400ES with an HT receiver (using HDMI for two and multi-channel playback).
It sounds good but can't touch what I got from a Rega Apollo with a BAT 300X-SE (through subbed Thiel 1.6).
I won't say the Sony is deficient until I hear it with the BAT but right now it sounds kind of generic.