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With regard to the left margin - unless you want a paragraph to be indented, I'd suggest setting the left margin to 0. All eReaders that I know of provide a margin of clear space around the area used to display the content on the screen, so you shouldn't need to specify a margin (unlike a printed page, where you need to specify the margin between the edge of the paper and print area).
With regard to the justification, I'm a bit confused - you say you set it to justify, but also refer to left align...? When you say the text is always on the right, do you mean it's right aligned, with a ragged left margin? Or just that there's a sizeable margin on the left?
Something else to check is whether the BLOCKQUOTE tag is being used around these paragraphs - that can result is a sizeable left indent on paragraphs when viewed on a Kindle or in the Kindle Previewer, and the amount of indent not so easy to control on the Kindle as it is in an EPUB file. Ideal for actual block quotes, but probably best avoided otherwise in a MOBI file.
Hope some of that helps.
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