Starting a new thread on this topic, spawned from this one:
http://forum.luminous-landscape.com/index.php?topic=123444.msg1030968#msg1030968.
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I might chime in with some info on MCT usage (on a Pro-1000), as I've recently spent a good deal of time testing out things in it that I cannot find properly documented.
A couple of starting points, some might be mentioned earlier, some might be new to some, some might be qualified speculation (missing hard facts from Canon).
Create calibration issues a feed adjustment, whether done or not in step 1. The reported values do _not_ agree, and the bug is reported to Canon (both the extra feed adjustment initiation, and the - much worse - discrepancy between the two runs). It _might_ be that the value reported in create calibration target is a delta to the one in step 1 (often low value for me), but not sure. Rerunning step 1 adjustments is fairly consistent. If different value from create calibration run is overwriting the one from step 1 is unknown. Canon is provided with am1x exported media files for examination but haven't returned with results. Please do your own bug reports to Canon if you replicate this issue to force some more pressure on the trouble solving.
Create calibration target does just that
. It just creates a target, but only the ability to later calibrate against it is registered, not an actual calibration. This might be (another) bug in MCT. As I recall from earlier tests some linearisation does change from this create calibration target, though calibration isn't reported until executed separately after target creation. I can dig out more data if needed. I've stopped using the calibration now, as changes seemed minor to end result of custom calibration, and since the extra feed adjustment it triggers seem buggy, and Canon has yet to come up with an explanation of the discrepancies.
For _some_ base media types the named quality scale if offset compared to built in media types, e.g. highest mean quality 2 for some media, but maps to quality 3 for others (in that case quality 2 can be set custom, but not as named setting). This is quite confusing. Quality range is 2-5, 2 being highest (see accounting manager).
Photo/glossy media cannot have a custom media type with the auto CO application as Pro Platinum which puts in from highlights to darks. The base media types for custom media seem to only apply to darker tones (as Glossy II). This has stopped me from using custom media for glossy papers, unfortunately - missing out on feed adjustments, named medias in selection and accounting etc. Overall/full setting still works, but often I just want auto, but with Pro Platinum CO curve, not the one excluding highlights where I think they matter a lot (perhaps more than shadows).
The three fine art base media type seem to render colors the same, and only differ in their default settings of ink limits and head height (and possible exclusion of rear feed for thicker papers). So the multiple options are just presets. Set back to same ink limit and head heights, they print the same. Also the Extra Heavy Art Paper base reported in MCT to use only MBK, is using a mix of PBK and MBK like the two others.
Only some base media types allow for use with "Contrast reproduction" in Print Studio Pro.
I'm sure there's more, but that's it for this time. Tons of time and testing for reaching some of this insight. All backed up by a lot of measurements and notes. Unfortunate, as I'd wished for all this to be clearly documented and resolved by Canon.
Please join with more knowledge and data.