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.