Hey Paulo,
that was a great catch, my cameras were in fact in ellipsoid heights instead of GEIOD88. Yet, surprisingly, that was NOT the main problem, myself overlooking, and Agisoft none-clear instructions!
The instructions below, miss a critical step to change Items: from All to Markers!
This is obvious, but when someone works with Detect Markers for the first time and following instructions to the comma, it is easy to overlook that selection option on the lower right corner of the frame- which cost me half a workday!
On p.88 of the manual under the title "Non-coded targets implementation"
[quotefor non-coded targets to be matched automatically, it is necessary to run align photos procedure first.
Non-coded targets.
Non-coded targets are more appropriate for aerial surveying projects due to the simplicity of the pattern
to be printed on a large scale.
When non-coded targets are detected Metashape allows automatic matching of detected non-coded targets
with referencing coordinates imported from file. To do that, when importing referencing coordinates
check the Ignore labels box in the Import CSV dialog. Metashape will try to match non-coded targets
markers with imported referencing coordinates markers, in case of success non-coded targets markers
will have corresponding coordinates. In case automatic matching does not work or works with errors,[/quote]
I wish Agisoft had the instructions above concise in bullet points and added in "Items" change to "Markers".