I'm wondering how the quality settings in CloneBD affect the encoding as it must be an issue with that which causes the obvious change every 1 second - I just checked a lower quality encode (I think the standard setting) and the change is faster than 1 second but is still there (just at a bit faster rate - BTW this might have been from an earlier version of CloneBD though so not certain it's the quality setting).
Well, the "1 second" is explained easily: that's the typical interval for key frames with Blu-ray discs (and it's pretty common in many video formats). And CloneBD encodes with that same key frame interval.
What you get with AVC is - a bit simplified: 1 key frame, which is a complete encoding of a picture, much like a jpeg.
Then the next 23 frames are encoded in reference to that key frame (and partly to each-other).
Roughly 24 frames per second, so that's that one second.
It's clear, that the further you go away from the key frame, the more the picture will degrade - until the next key frame arrives.
But that is usually only perceptible at very low bit rates. With higher bit rates, that degrading effect is very minimal.
Does something happen with the encoding at regular second or so intervals ? Maybe the bitrate is only changed every second?
No, CloneBD doesn't change the bitrate during transcoding.
Found the perfect example of this on youtube....watch this video at 240p resolution FULL SCREEN and watch the playstation logo (red green and blue blurry thing where it says PlayStation Classic on the purple header)
Yes, I can see it, but really only at very low bit rate/resolution and that's normal and to be expected.
I can not see it on any video encoded by CloneBD with nVidia, though.
Since you say, you're encoding at 5-6mbps, there's your cause.
That really is low for 1080p - it's fine for watching, if your expectations aren't too high, but if that didn't have any drawbacks, there would be no point in encoding at higher bit rates, would there?
Anyway: CloneBD can't do anything about this, it's entirely out of its hands.
If software encoding does it better at the same rate, then hats off to the developers of x264 - then again, x264 is known to be pretty good.