I very recently took over custodianship of a drupal CiviCRM, so I don't really have a clue what I'm doing. Bear with me.
I'm on civi 4.6.2 on drupal, and ever since the upgrade, the mailings have gone completely haywire on me. back when I could upload a .html file, everything worked fine, but now, it's all wonky.
When I first paste the html in, everything looks fine in the WYSIWYG screen, but when I save it, one of several things happens: It simply doesn't save the changes to the HTML email field (though the new subject and plaintext fields save perfectly fine). Once, I got it to save the HTML, but it stripped out large chunks of that, and put in the HTML Special entity codes next to a bunch (but not all) of the spaces and quotation marks, but still preserved the actually spaces and quotation marks.