Hi! I tried searching for this problem on the board but I only found an empty thread from three years ago.
I use the command line conversion utility on a Linux Mint 17 machine using calibre 2.1.0. I have a Markdown-formatted txt file. I'll copy the command below so you see the exact settings I'm using.
Code:
ebook-convert mybook.txt mybook.azw3 --remove-paragraph-spacing --remove-paragraph-spacing-indent-size 1.0 --output-profile kindle_pw --formatting-type markdown --paragraph-type off --markdown-extensions tables --extra-css "custom_markdown.css"
But my custom CSS just won't be used. I tried it with --extra-css="custom_markdown.css" or without quotes... no luck. The conversion runs through fine (no errors whatsoever) and the CSS itself isn't corrputed either. I can open the azw3 file with the graphical editor and paste my CSS into one of the two css files and it works then. But not from the command line.
Just putting it here, it might be worth looking into.