Preserve Formatting Doesn't Always Work

Preserved formatting works when I compile to pdf, but not when I compile to mobi format. Checked the manual, but nothing. Is it the KindleGen?

There is formatting that the standard e-reader formats cannot replicate, as it’s based on HTML, and so is more limited than a layout program designed for the printed page.

So it really depends on what formatting you are trying to preserve. I’d look into documentation about the mobi format to see if it’s even possible, and then come back and ask how to make Scrivener output that kind of formatting.