@Switch Blayde
For Kindle, are you guys uploading MOBI or AZW3 format?
Mobi on Bookapy
According to Lazeez, the only benefit to AZW is the ability to lock (DRM) the file so no more than a single reader can access it. Thus he's publicly stated that MOBI is the ONLY Amazon format that Bookapy will accept.
For Mobi, it defaults to justified even if the Word doc I input to Calibre has it as left.
Despite Lazeez's misgivings (he hates justified text, I typically justify everything, and have never had any trouble getting it to accept it.
As usual, the key is to define the behavior in each paragraphs CSS Style Definitions, which I believe you're already doing, so there must be some other conflict that's inhibiting the justification.