I am not sure if it should do so. The checkbox is about the "quality" check. -
the plug-in does not preserve the subsampling setting, if everything else is unchanged - the default of 4:4:4 is always used, even if the image was read form a JPG file with a different subsampling.

On the other hand, the tooltip hint for that control seems to imply that subsampling should indeed be preserved. Are there any other options that should be inclded in this?

If I'm selecting "Use quality settings from original image" the subsampling is always changed back to its original value (which is not always 4:4:4).

Edit: I can't change the status from NEEDINFO to UNCONFIRMED (an error message says that I'm not allowed to set the "Ever confirmed" field from 1 to 0) and setting the status to RESOLVED would be currently not correct.

Ok - I could notice the misbehavior this time around - and there are indeed inconsistencies. I saw another problem beyond your report that is

- On re-exporting an JPEG (export as), the "subsambling" setting does not reflect the subsampling that the original image had, even though the "use quality settings from the original image" box is checked. The "Quality" itself does properly reflect that quality setting.

- On toggling off the "use quality settings..." and turning it back on again, the subsampling value does change to  the one in the original image. 

This is a bug: the subsampling setting should be the same by default (or "use same settings" be off by default)

Now the specific issue you describe is that besides that: 

- Manually changing the "quality setting" automatically checks off the "use same setting..." toggle; but changing the "Subsample"  does not do so. 

- but when toggling "use same setting" back on, the "subsample" value is restored to the previous one

The fix should be: 

Keep the "Subsample" setting always consistent with the "use quality settings from the original image" checkbox.

(In reply to Joao S. O. Bueno from comment #4)
> - On toggling off the "use quality settings..." and turning it back on
> again, the subsampling value does change to  the one in the original image. 
> 
> This is a bug: the subsampling setting should be the same by default (or
> "use same settings" be off by default)

Is this really a bug? Would it not be plausible to set the subsampling to the original value of the JPG that gets overwritten if "Use quality settings from original image" gets selected? Also your found re-exporting bug implies that.

The current state is unidirectional: Changing checkbox could change option; Changing option never changes checkbox.
The state that I thought it should be is bidirectional (as it is currently done with the quality slider): Changing checkbox could change option; Changing option could change checkbox.
The state that you think it should be is unbinding this option (except on the initialization process on re-exporting): Changing checkbox never changes option; Changing option never changes checkbox.

Or have I just misunderstood something?

I was going to report this bug when I found this. IMHO the chroma setting should work exactly like the quality slider. When you check the "Use ... initial..." box, this sets the slider to the initial value, and if you move the slider, this resets the "Use ... initial..." option. 

It appears that setting the "Use ... initial..." option currently also sets the Chroma subsampling to the initial value, so changing the CS value should reset "Use ... initial..." option.

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