My source material is EPUB, which I then convert to dual-mobi via Calibre.
I typically set top and bottom margins around chapter heads. I used to use %, then discovered this resulted in missing chapter heads and text in the mobi portion (though the kf8 portion is fine). Switching to em solved this problem.
When I looked in the Kindle Publishing Guidelines, I found: "When using the margin and padding CSS properties, specify the values in percentage (%) instead of em units"

(section 3.1.7 on page 15).
Does anyone here use % with margins such that it works with both mobi and kf8? Any idea what I might be doing wrong?
Examples
Spoiler:
This results in missing chapter heads and text when converted to mobi (but works fine in kf8):
Code:
h1 {
font-size: 120%;
margin-top: 20%;
margin-bottom; 10%;
text-align: center;}
But if I change it to em, it works for both mobi and kf8:
Code:
h1 {
font-size: 120%;
margin-top: 2em;
margin-bottom; 1em;
text-align: center;}