I've never owned a Kindle so I don't know much about the mobi format, but what I do know is that mobis have very limited styling capabilities. The margin-right property is one (of many) which is unsupported. So that might explain half your problem.
For margin-left, I think this is achieved by using nested <blockquote> tags, but maybe Calibre takes care of all that during the conversion epub to mobi.
One more thing is that there is an 'Ignore margins' checkbox on the Convert - MOBI output page. Try your conversion with both settings and see what difference it makes to your output mobi.
If none of this is helpful perhaps someone who knows more about mobi will drop by.