@Baja - glad you found the info useful.
As for "Ignore Margins", to be perfectly honest I don't know exactly what this does, I would have to look at the code. I've done a google and can't find an explanation either and the tooltip is too vague/ambiguous. To my mind there are two possible things it might be doing:
(1) It sets to zero the default 5pt left/right and top/bottom margins that calibre sets for the page when doing conversions. Since the Kindle already has it's own "margin" setting on the device, it is redundant to insert additional margins in the document for the standard page. However I don't see how this would solve your problem, because if a large left margin is set on a style at paragraph level (like a blockquote tag) then this would not change that.
(2) That it looks for margin-left in the css file and setting this to zero. This would brute force solve your problem, at the cost of trashing the style for text that was important to be indented, as per my last post. If it did that I would certainly stay away from that setting.
It was HarryT that recommended the setting, perhaps he or someone else may have some insight into what it does. If it does (1) then it is safe to use but won't solve your issue in my opinion, and if it is (2) I wouldn't recommend it.