The problem lies not so much in justification as in hyphenation.
The Kindle software does not automatically hyphenate long words. It might therefore need to force long words onto the next line. If, as a result, the previous line (the one that would have contained the hyphen) is unusually short, the software doesn't attempt to justify it.
This might be annoying, but it's probably the right choice. You get a ragged line ending, rather than a justified line with a large amount of white space in the middle of it.
The problem is particularly bad where two words are joined by an em dash with no spaces between. The software sees these as a single word, and so the above behaviour kicks in.
At least, that's my understanding of the problem. If I've got it wrong, no doubt someone will correct me.
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