[DoctorOhh]

I may be far off base with my limited knowledge of HTML but I'm going to take a stab at this anyways.

Originally Posted by therealjoeblow

I don't want it to do that, as it effectively gives me a full line blank space in between the 2 lines where the break occurs, I just want it to retain the simple line break.

Is there a config option to disable this?

No, calibre is converting what you give it. There is an unseen line break after every comma that calibre properly replaces with the functional equivalent of
<br class="calibre1" /> (notice the self-closing / these aren't optional) and leaves your improper tag of <br> in place unaltered.

First, you should be using <br /> not <br>

Originally Posted by therealjoeblow

<p class="indentedquote">This is some quoted passage,
<br>This is the next line in the quote,
<br>and yet another line,
<br>and the final line in the quote.</p>

Second the above is incorrect it should be the following.

Originally Posted by therealjoeblow

<p class="indentedquote">This is some quoted passage,<br />
This is the next line in the quote, <br />
and yet another line,<br />
and the final line in the quote.</p>

What happens is you convert it this way.

I'm also curious what format are you converting from/to?