Well, there is an option under the comic input conversion preference that will tell calibre to not sort the items by name, but that should be unchecked by default. I suspect it's more a case of needing to include all 3 digits in each file. In other words, they should be named as follows:
001.jpg
002.jpg
...
010.jpg
...
100.jpg
I can confirm that this is required in Linux.
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