Okay, I've been investigating my dropped frames issue since November whenever I had some time, and finally today I singled it out to my 609. I also have only seen it on 1080p/24. I've also tried all combinations of Through, Direct, Lip Sync, audio delay, send audio to tv, etc, and can not resolve the issue.
Subjectively, it seems as if it wasn't happening, then started out of the blue one day and has progressively gotten worse (more often). I don't have proof of that, though, as it wasn't until today that I actually measured it occurring every 2 minutes and 47 seconds, plus or minus one second. I can power on my system, go to the credits chapter on any 23.976p Blu-ray, and just watch the credits until I see the skip. I then start my watch timer, and every 2 minutes 47 seconds like clockwork it will skip - I can rewind, pause my Blu-ray, etc. For example, as soon as I see the skip on the credits, I start my watch, then pause the disc. At about 2 minutes 27 seconds I unpause, and then the skip comes right on time at 2:47 after the previous one. I can also not pause at all and just let it run.
I've also only seen it when the source is outputting 23.976p and the TV indicates this as well. I've tried 1080p60 and 1080i60, and it doesn't happen.
In order to further test this, I created myself an AVCHD disc that just plays a scrolling object for 10 minutes. Then this is what I've tried with that disc:
Oppo BDP-93 to 609 to JVC RS40 projector: Skip occurs
Oppo BDP-93 straight to projector: No skip
HDMI computer output to 609 to projector: Skip occurs
HDMI computer straight to projector: No skip
It seems definitive that the 609 is the culprit here, and I'm even more confident now that others are reporting this will other Blu-ray players and displays.
I've also recorded the screen with a video camera and verified it skips a single frame in the video when it occurs.
I'll try to call Onkyo as well when I get the time.