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convert -size 64x64 xc: xc: xc: -gravity northwest ^
-pointsize 24 -annotate +0+0 "%[fx:t+1]" +gravity -crop 2x1@ out6.png
Annotate is numbering the panels 1, 3, and 5 as if it's counting relative to the six images in the stack after the crop, even though the annotate operation occurs before the crop and should only affect the original three images.
If I run the same command with IM 7.0.7-8 by substituting "magick" for "convert", the output is as expected with the panels numbered 1, 2, and 3.