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This sounds like some stuff I've seen. Chances are real good that there's a tag somewhere that just ain't right and RoboHelp "fixed" it the wrong way. Run it through an online HTML validator--it uploads the file and will tell you more than you will ever need. Some stuff will not look the same in WYSiWYG as it does when compiled.
Thanks, that was indeed the problem. For some reason it closed some of the tags correctly and not the others.
Another quick question...I reformatted the H2 and H3 headers so that they have different highlighting, size, etc. and indent a certain amount. In the WYSIWYG these look fine, but when I generate my project, they format correctly as far as looks, but they don't indent properly (they simply left-justify). How do I force them to indent in my generated project?
Imported PDFs always throw up some strange formatting.
You said that you had deleted the styles created when you imported the document. Are you still using the created style sheet? If so, that is the most likely problem. If you have a working stylesheet from another project, you could try importing it into your project and re-create the styles you need or create a new style sheet.
As a quick fix, you could try editing the true code by adding the stye=... to your <h2>
<h2 style="margin-left: 40px;">TEXT</h2>
40pixels is the default indent.