The most likely explanation for the problem is that when the Onkyo has its video processing active (which apparently it does even when it is in Through or Direct modes) it is taking a 23.976 input (which is the standard for NTSC Blu-Rays) and it is outputting them to the display at 24.00 FPS.
If you take a 23.976 input signal and send it out as 24.00 fps then you will drop a frame about every 40 seconds. Whether or not you see the dropped frame depends on a lot of things, like, the frequency of the TV (some TVs with 120hz processing and/or motion smoothing might make the problem less noticeable but also make the movie look more "video-like" with what is often described as a soap opera video effect), what is happening on-screen at the time of the frame-drop (action vs a static shot), etc.
I should point out that many people won't notice a problem like this. They either don't have their TV set up for 24P playback, they have a lot of video processing turned on, or they simply don't notice video glitches. For someone like me who really likes film, has a high end 24P capable display that is very large, and has the TV set up in a calibrated ISF mode displaying at a 24P multiple (in my case 96hz and 60hz both actually show the problem) then the problem is very irritating because you see a small stutter during playback every so often, making playback look "jerky".
I can't test with 24.00 because I don't have any 24.00 content. All north american Blu-ray discs should be mastered at 23.976 FPS.
One way to test this problem out would be to connect a TV or test set to the HDMI output of the Onkyo that displays the EXACT frame-rate it is receiving. If a US blu-ray source at "24FPS" is being sent to the Onkyo, it is actually a 23.976 signal, and that should be shown on the TV or test unit receiving the signal from the Onkyo and display "23.976" but I expect it would actually show "24.000"... proving that there is a breakage.