Image magick convert ignores some images - imagemagick

Question

I am using this command to flatten 3 images in a folder.
for pos1 in 1*.png; do for pos3 in 3*.png; do for pos6 in 6*.png; do convert -gravity center $pos1 $pos3 $pos6 -layers flatten $pos1$pos3$pos6 ;done ;done ;done
this is how my folder looks:
For some reason, imagemagick ignores the 1*.png images and creates a composition of just $pos3 and $pos6. What could be the reason for this behaviour and how do I fix it? The images i am manipulating are the product of some older image magick manipulation.
UPDATE:
After some more testing it looks like that the error comes from the fact that the input images are the output of come previous convert / composite command (cant remember which one I used). Still, I don't know how to fix this problem.
identify command output (no histogram):
Format: PNG (Portable Network Graphics)
Mime type: image/png
Class: DirectClass
Geometry: 3843x3402+0+0
Units: Undefined
Type: TrueColorAlpha
Endianess: Undefined
Colorspace: sRGB
Depth: 8-bit
Channel depth:
red: 8-bit
green: 8-bit
blue: 8-bit
alpha: 1-bit
Channel statistics:
Pixels: 13073886
Red:
min: 0 (0)
max: 255 (1)
mean: 246.072 (0.96499)
standard deviation: 44.204 (0.173349)
kurtosis: 23.2206
skewness: -4.96363
entropy: 0.0669139
Green:
min: 0 (0)
max: 255 (1)
mean: 246.072 (0.96499)
standard deviation: 44.2038 (0.173348)
kurtosis: 23.2205
skewness: -4.96362
entropy: 0.0669169
Blue:
min: 0 (0)
max: 255 (1)
mean: 246.072 (0.96499)
standard deviation: 44.2038 (0.173348)
kurtosis: 23.2207
skewness: -4.96364
entropy: 0.066917
Alpha:
min: 255 (1)
max: 255 (1)
mean: 255 (1)
standard deviation: 0 (0)
kurtosis: 0
skewness: 0
entropy: 0
Image statistics:
Overall:
min: 0 (0)
max: 255 (1)
mean: 184.554 (0.723742)
standard deviation: 38.2817 (0.150124)
kurtosis: 150.659
skewness: -25.8099
entropy: 0.050187
Rendering intent: Perceptual
Gamma: 0.45455
Chromaticity:
red primary: (0.64,0.33)
green primary: (0.3,0.6)
blue primary: (0.15,0.06)
white point: (0.3127,0.329)
Background color: white
Border color: srgba(223,223,223,1)
Matte color: grey74
Transparent color: none
Interlace: None
Intensity: Undefined
Compose: Over
Page geometry: 3843x3402+0+0
Dispose: Undefined
Iterations: 0
Compression: Zip
Orientation: Undefined
Properties:
date:create: 2017-04-05T20:18:59+02:00
date:modify: 2017-04-05T10:36:08+02:00
png:bKGD: chunk was found (see Background color, above)
png:cHRM: chunk was found (see Chromaticity, above)
png:gAMA: gamma=0.45454544 (See Gamma, above)
png:IHDR.bit-depth-orig: 8
png:IHDR.bit_depth: 8
png:IHDR.color-type-orig: 6
png:IHDR.color_type: 6 (RGBA)
png:IHDR.interlace_method: 0 (Not interlaced)
png:IHDR.width,height: 3843, 3402
png:sRGB: intent=0 (Perceptual Intent)
png:text: 2 tEXt/zTXt/iTXt chunks were found
png:tIME: 2017-04-03T18:20:37Z
signature: ea0ce8b483b92bda18d999d203a5e1329d48fb63059d6702051b74f7930286fc
Artifacts:
filename: /Users/mainuser/Desktop/final/HALFS/to/1_1ND1_1.png
verbose: true
Tainted: False
Filesize: 710KB
Number pixels: 13.07M
Pixels per second: 54.47MB
User time: 0.230u
Elapsed time: 0:01.240
Version: ImageMagick 6.9.7-3 Q16 x86_64 2017-01-07 http://www.imagemagick.org

Answer 1

Updated Answer
As we are having some problems and you can't share your images, let's make some of our own:
convert -size 600x200 xc:none -fill red -draw "circle 100,100 100,200" -bordercolor black -border 1 1.png
convert -size 600x200 xc:none -fill lime -draw "circle 300,100 400,100" -bordercolor black -border 1 2.png
convert -size 600x200 xc:none -fill blue -draw "circle 500,100 600,100" -bordercolor black -border 1 3.png
Now let's flatten them onto a transparent background:
convert [123].png -background none -flatten result.png
Maybe you can create these images and try with your version of ImageMagick.
Original Answer
It depends on how your files are in terms of size and transparency, but try this in the middle of your loop:
convert -gravity center "$pos1" "$pos3" -composite "$pos6" -composite "${pos1}${pos3}${pos6}.png"
This assumes that "$pos1" is the largest file in terms of pixel dimensions.
Note that you should always double quote shell variables when expanding them in case your filenames happen to have spaces in them.

Answer 2

This is not the answer to the original question but I found it because I had the same problem that images were just ignored when using convert.
My solution was allocate higher ressources in resources.xml as described in this solution.
Maybe this is useful to someone at some point.