Okay, here's the conversion log for the .epub --> .mobi conversion of the full file:

Convert book 1 of 1 (Falling Free [Vorkosigan #1])
Resolved conversion options
calibre version: 0.7.1
{'asciiize': False,
'author_sort': None,
'authors': None,
'base_font_size': 0.0,
'book_producer': None,
'change_justification': u'original',
'chapter': u"//*[((name()='h1' or name()='h2') and re:test(., 'chapter|book|section|part\\s+', 'i')) or @class = 'chapter']",
'chapter_mark': u'pagebreak',
'comments': None,
'cover': 'c:\\users\\(username)\\appdata\\local\\temp\\cali bre_0.7.1_yxi48m.jpeg',
'debug_pipeline': None,
'disable_font_rescaling': False,
'dont_compress': False,
'extra_css': None,
'font_size_mapping': None,
'footer_regex': u'(?i)(?<=<hr>)((\\s*<a name=\\d+></a>((<img.+?>)*<br>\\s*)?\\d+<br>\\s*.*?\\s*)|(\\s* <a name=\\d+></a>((<img.+?>)*<br>\\s*)?.*?<br>\\s*\\d+))(?=<br>)' ,
'header_regex': u'(?i)(?<=<hr>)((\\s*<a name=\\d+></a>((<img.+?>)*<br>\\s*)?\\d+<br>\\s*.*?\\s*)|(\\s* <a name=\\d+></a>((<img.+?>)*<br>\\s*)?.*?<br>\\s*\\d+))(?=<br>)' ,
'input_encoding': None,
'input_profile': <calibre.customize.profiles.InputProfile object at 0x05123B30>,
'insert_blank_line': False,
'insert_metadata': False,
'isbn': None,
'keep_ligatures': False,
'language': None,
'level1_toc': None,
'level2_toc': None,
'level3_toc': None,
'line_height': 0.0,
'linearize_tables': False,
'margin_bottom': 5.0,
'margin_left': 5.0,
'margin_right': 5.0,
'margin_top': 5.0,
'max_toc_links': 50,
'no_chapters_in_toc': False,
'no_inline_navbars': True,
'no_inline_toc': True,
'output_profile': <calibre.customize.profiles.KindleOutput object at 0x05123E10>,
'page_breaks_before': u'/',
'personal_doc': u'[PDOC]',
'prefer_author_sort': False,
'prefer_metadata_cover': False,
'preprocess_html': False,
'pretty_print': False,
'pubdate': None,
'publisher': None,
'rating': None,
'read_metadata_from_opf': 'c:\\users\\(username)\\appdata\\local\\temp\\cali bre_0.7.1_yice0w.opf',
'remove_first_image': False,
'remove_footer': False,
'remove_header': False,
'remove_paragraph_spacing': False,
'remove_paragraph_spacing_indent_size': 1.5,
'rescale_images': False,
'series': None,
'series_index': None,
'tags': None,
'timestamp': None,
'title': None,
'title_sort': None,
'toc_filter': None,
'toc_threshold': 6,
'toc_title': None,
'use_auto_toc': False,
'verbose': 2}
InputFormatPlugin: EPUB Input running
on C:\Users\(username)\Documents\E-Book Library\Calibre Archive\Bujold_ Lois McMaster\Falling Free [Vorkosigan #1] (6)\Falling Free [Vorkosigan #1] - Bujold_ Lois McMaster.epub
Parsing all content...
Parsing OEBPS/Text/Chap13.xhtml ...
Parsing OEBPS/Styles/StyleTitle.css ...
Parsing OEBPS/Text/AboutAuthor.xhtml ...
Parsing OEBPS/Text/Chap02.xhtml ...
Parsing OEBPS/Text/Chap06.xhtml ...
Parsing OEBPS/Text/Chap09.xhtml ...
Parsing OEBPS/Text/Summary.xhtml ...
Parsing OEBPS/Text/Chap15.xhtml ...
Parsing OEBPS/Text/Dedication.xhtml ...
Parsing OEBPS/Text/TOC.xhtml ...
Parsing OEBPS/Text/Chap08.xhtml ...
Parsing OEBPS/Text/Chap14.xhtml ...
Parsing OEBPS/Text/Chap12.xhtml ...
Parsing OEBPS/Text/Chap11.xhtml ...
Parsing OEBPS/Text/Chap01.xhtml ...
Parsing OEBPS/Text/Chap05.xhtml ...
Parsing OEBPS/Text/Chap04.xhtml ...
Parsing OEBPS/Text/Chap03.xhtml ...
Parsing OEBPS/Text/Chap07.xhtml ...
Parsing OEBPS/Text/Chap10.xhtml ...
Parsing OEBPS/Styles/StyleNovel.css ...
Parsing OEBPS/Text/TitlePage.xhtml ...
Parsing OEBPS/Text/Chap16.xhtml ...
Reading TOC from NCX...
Merging user specified metadata...
Detecting structure...
Detected chapter: Book 1 of the Vorkosigan Saga
Detected chapter: Chapter 1
Detected chapter: Chapter 2
Detected chapter: Chapter 3
Detected chapter: Chapter 4
Detected chapter: Chapter 5
Detected chapter: Chapter 6
Detected chapter: Chapter 7
Detected chapter: Chapter 8
Detected chapter: Chapter 9
Detected chapter: Chapter 10
Detected chapter: Chapter 11
Detected chapter: Chapter 12
Detected chapter: Chapter 13
Detected chapter: Chapter 14
Detected chapter: Chapter 15
Detected chapter: Chapter 16
Flattening CSS and remapping font sizes...
Source base font size is 12.00000pt
Cleaning up manifest...
Trimming unused files from manifest...
Parsing stylesheet.css ...
Creating MOBI Output...
Applying case-transforming CSS...
Parsing manglecase.css ...
Rasterizing SVG images...
Converting XHTML to Mobipocket markup...
Serializing markup content...
Compressing markup content...
Generating flat CTOC ...
CNCX utilization: 1 record, 0% full
Indexing navPoints ...
Generating INDX ...
Serializing images...
MOBI output written to c:\users\(username)\appdata\local\temp\calibre_0.7 .1_77sswn.mobi