There seems to be a bug in the handling of "@" on the command line. Briefly: when the filename starts with a drive (like "h:"), convert doesn't process the file correctly.
My command is:
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"%IMG685%convert" h:\farmThing\cl_temp\Redfile1.png @h:\farmThing\cl_temp\crop1.txt NULL:
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( +clone -crop 64x54+0+0 +repage -write h:\farmThing\cl_temp\crop_R5_0.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_0.txt +delete )
( +clone -crop 64x54+64+0 +repage -write h:\farmThing\cl_temp\crop_R5_1.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_1.txt +delete )
( +clone -crop 64x54+128+0 +repage -write h:\farmThing\cl_temp\crop_R5_2.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_2.txt +delete )
( +clone -crop 64x54+192+0 +repage -write h:\farmThing\cl_temp\crop_R5_3.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_3.txt +delete )
( +clone -crop 64x54+256+0 +repage -write h:\farmThing\cl_temp\crop_R5_4.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_4.txt +delete )
( +clone -crop 64x54+320+0 +repage -write h:\farmThing\cl_temp\crop_R5_5.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_5.txt +delete )
( +clone -crop 64x54+0+54 +repage -write h:\farmThing\cl_temp\crop_R5_6.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_6.txt +delete )
( +clone -crop 64x54+64+54 +repage -write h:\farmThing\cl_temp\crop_R5_7.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_7.txt +delete )
( +clone -crop 64x54+128+54 +repage -write h:\farmThing\cl_temp\crop_R5_8.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_8.txt +delete )
( +clone -crop 64x54+192+54 +repage -write h:\farmThing\cl_temp\crop_R5_9.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_9.txt +delete )
( +clone -crop 64x54+256+54 +repage -write h:\farmThing\cl_temp\crop_R5_10.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_10.txt +delete )
( +clone -crop 64x54+320+54 +repage -write h:\farmThing\cl_temp\crop_R5_11.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_11.txt +delete )
( +clone -crop 64x54+0+108 +repage -write h:\farmThing\cl_temp\crop_R5_12.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_12.txt +delete )
( +clone -crop 64x54+64+108 +repage -write h:\farmThing\cl_temp\crop_R5_13.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_13.txt +delete )
( +clone -crop 64x54+128+108 +repage -write h:\farmThing\cl_temp\crop_R5_14.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_14.txt +delete )
( +clone -crop 64x54+192+108 +repage -write h:\farmThing\cl_temp\crop_R5_15.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_15.txt +delete )
( +clone -crop 64x54+256+108 +repage -write h:\farmThing\cl_temp\crop_R5_16.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_16.txt +delete )
( +clone -crop 64x54+320+108 +repage -write h:\farmThing\cl_temp\crop_R5_17.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_17.txt +delete )
( +clone -crop 64x54+0+162 +repage -write h:\farmThing\cl_temp\crop_R5_18.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_18.txt +delete )
( +clone -crop 64x54+64+162 +repage -write h:\farmThing\cl_temp\crop_R5_19.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_19.txt +delete )
( +clone -crop 64x54+128+162 +repage -write h:\farmThing\cl_temp\crop_R5_20.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_20.txt +delete )
( +clone -crop 64x54+192+162 +repage -write h:\farmThing\cl_temp\crop_R5_21.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_21.txt +delete )
( +clone -crop 64x54+256+162 +repage -write h:\farmThing\cl_temp\crop_R5_22.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_22.txt +delete )
( +clone -crop 64x54+320+162 +repage -write h:\farmThing\cl_temp\crop_R5_23.miff -format "%[fx:standard_deviation]" -write info:h:\farmThing\cl_temp\sd1_R5_23.txt +delete )
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convert.exe: unable to open image `(': No such file or directory @ error/blob.c/
OpenBlob/2641.
convert.exe: no decode delegate for this image format `(' @ error/constitute.c/R
eadImage/550.
convert.exe: unable to open image `+clone': No such file or directory @ error/bl
ob.c/OpenBlob/2641.
convert.exe: no decode delegate for this image format `+clone' @ error/constitut
e.c/ReadImage/550.
Moving crop1.txt to directory "temp\" and executing this...
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"%IMG685%convert" h:\farmThing\cl_temp\Redfile1.png @temp\crop1.txt NULL: