What are you using to build/compile your MOBI?
First off... there are no "real" margins in the MOBI format. Left margins are simulated using the blockquote element. The blockquotes can be nested to obtain "deeper" left margins.
So in the process of building your MOBI from the html/css source, the margin-left css property is simply being converted to blockquote elements in the MOBI's internal markup code.
The best way of being able to control the depths of your margins is to completely forego the css left-margin approach and just start with the blockquotes (nested if need be) to begin with. They're going to end up that way in the final MOBI anyway.
(and yes, those blockquotes will render different indent "depths" on different devices/apps)