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That means your <p> tags probably have some other style, applied, or that your document uses <div> tags instead of <p> tags - you would need to enable debug and look at your html output in the debug directory to figure out what to do.
If it's some other style you could do this once you know the style name:
p.stylename {text-indent:3%}
You could also try em instead of percent, not sure if it makes a difference for mobi output:
p {text-indent:1.5em}
Regarding your other question, yes, just convert from mobi to mobi again. However many users convert from mobi to epub - edit the book to meet their liking using Sigil, then convert the epub back to mobi.
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