I'm confused because of the representation of mbtiles files in QGIS. It seems that the whole grid is shifted by about 3 m to the south.
So far I can observe this behavior only in the context of QGIS and mbtiles. Maybe somebody comes up with an idea?
For reverse engineering: Load Geotiff in Tilemill and export as mbtiles. Load both files in QGIS.
On the search for the cause I have
generated the mbtiles file with geoscript-groovy: same result -> Tilemill does not seem to be the cause.
taken an other GeoTIF -> same result: shifted 3m south.
loaded the mbtiles-file in MapProxy, published it as WMS and loaded it in QGIS -> fits perfectly: the mbtiles file itself it seems so not to be the cause.