MOBI: No Table of Contents

I download fanfics using FanfictionLoader, and I've found this to be a consistent problem:

If I download as MOBI, (eg: http://www.mediafire.com/?1fh3d38t0zqhd5l ) W/O CONVERTING IN CALIBRE, THE INCL. TOC WORKS.

If I convert from MOBI to MOBI (to create chapter markers), THE INCLUDED TOC IS NOT DETECTED.

If I convert from MOBI to EPUB to MOBI, THE INCLUDED TOC IS NOT DETECTED.

If I convert from MOBI to EPUB, edit in Sigil and rename the .html file on which the TOC is located, then convert from EPUB to MOBI, THE TOC WORKS.

I'm not sure what the problem is, but it would seem that merely renaming the TOC's file (via EPUB) fixes the problem. I've even confirmed this by editing the EPUB and re-renaming the file back to it's original name to find that converting to MOBI breaks the TOC again.

Here is a log of MOBI to MOBI which broke the included TOC:

Convert book 1 of 1 (Creature of Habit)
Resolved conversion options
calibre version: 0.7.52
{'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' or name()='h3') and re:test(., 'chapter|book|section|part|prologue|epilogue\\s+', 'i')) or @class = 'chapter']",
 'chapter_mark': u'pagebreak',
 'comments': None,
 'cover': None,
 'debug_pipeline': None,
 'dehyphenate': True,
 'delete_blank_paragraphs': True,
 'disable_font_rescaling': False,
 'dont_compress': False,
 'enable_heuristics': False,
 'extra_css': None,
 'fix_indents': True,
 'font_size_mapping': None,
 'format_scene_breaks': True,
 'html_unwrap_factor': 0.4,
 'input_encoding': None,
 'input_profile': <calibre.customize.profiles.InputProfile object at 0x059AABF0>,
 'insert_blank_line': True,
 'insert_metadata': False,
 'isbn': None,
 'italicize_common_cases': True,
 'keep_ligatures': True,
 'language': None,
 'level1_toc': u"//*[name()='h1']",
 'level2_toc': u"//*[name()='h2']",
 'level3_toc': u"//*[name()='h3']",
 'line_height': 0.0,
 'linearize_tables': True,
 'margin_bottom': 5.0,
 'margin_left': 5.0,
 'margin_right': 5.0,
 'margin_top': 5.0,
 'markup_chapter_headings': True,
 'max_toc_links': 0,
 'minimum_line_height': 120.0,
 'mobi_ignore_margins': False,
 'no_chapters_in_toc': True,
 'no_inline_navbars': True,
 'no_inline_toc': True,
 'output_profile': <calibre.customize.profiles.KindleOutput object at 0x059AAF10>,
 'page_breaks_before': u"//*[name()='h1' or name()='h2' or name()='h3']",
 'personal_doc': u'[PDOC]',
 'prefer_author_sort': False,
 'prefer_metadata_cover': False,
 'pretty_print': False,
 'pubdate': None,
 'publisher': None,
 'rating': None,
 'read_metadata_from_opf': 'c:\\users\\david\\appdata\\local\\temp\\calibre_0.7.52_tmp_erwfjq\\calibre_0.7.52_c0i9ou.opf',
 'remove_fake_margins': True,
 'remove_first_image': False,
 'remove_paragraph_spacing': True,
 'remove_paragraph_spacing_indent_size': 1.5,
 'renumber_headings': True,
 'replace_scene_breaks': u'',
 'rescale_images': False,
 'series': None,
 'series_index': None,
 'smarten_punctuation': True,
 'sr1_replace': None,
 'sr1_search': None,
 'sr2_replace': None,
 'sr2_search': None,
 'sr3_replace': None,
 'sr3_search': None,
 'tags': None,
 'timestamp': None,
 'title': None,
 'title_sort': None,
 'toc_filter': None,
 'toc_threshold': 6,
 'toc_title': None,
 'unwrap_lines': True,
 'use_auto_toc': False,
 'verbose': 2}
InputFormatPlugin: MOBI Input running
on C:\Users\Public\Dropbox\Public\eBook_Library\EZRocksAngel\Creature of Habit (435)\Creature of Habit - EZRocksAngel.azw
Extracting text...
Adding anchors...
Extracting images...
Cleaning up HTML...
Parsing HTML...
Converting style information to CSS...
Creating OPF...
Parsing all content...
Parsing styles.css ...
Parsing Creature%20of%20Habit.html ...
Forcing Creature%20of%20Habit.html into XHTML namespace
Guide reference 'Creature of Habit.html#filepos1147' not found
Reading TOC from NCX...
Merging user specified metadata...
Detecting structure...
 Detected chapter: 1. Chapter 1
 Detected chapter: 2. Chapter 2
 Detected chapter: 3. Chapter 3
 Detected chapter: 4. Chapter 4
 Detected chapter: 5. Chapter 5
 Detected chapter: 6. Chapter 6
 Detected chapter: 7. Chapter 7
 Detected chapter: 8. Chapter 8
 Detected chapter: 9. Chapter 9
 Detected chapter: 10. Chapter 10
 Detected chapter: 11. Chapter 11
 Detected chapter: 12. Chapter 12
 Detected chapter: 13. Chapter 13
 Detected chapter: 14. Chapter 14
 Detected chapter: 15. Chapter 15
 Detected chapter: 16. Chapter 16
 Detected chapter: 17. Chapter 17
 Detected chapter: 18. Chapter 18
 Detected chapter: 19. Chapter 19
 Detected chapter: 20. Chapter 20
 Detected chapter: 21. Chapter 21
 Detected chapter: 22. Chapter 22
 Detected chapter: 23. Chapter 23
 Detected chapter: 24. Chapter 24
 Detected chapter: 25. Chapter 25
 Detected chapter: 26. Chapter 26
 Detected chapter: 27. Chapter 27
 Detected chapter: 28. Chapter 28
 Detected chapter: 29. Chapter 29
 Detected chapter: 30. Chapter 30
 Detected chapter: 32. Chapter 32
Flattening CSS and remapping font sizes...
Source base font size is 12.00000pt
Removing fake margins...
Parsing stylesheet.css ...
Found 66 items of level: div_1
Found 63 items of level: div_2
Found 4960 items of level: p_3
Found 1 items of level: p_1
Ignoring level p_1
div_1 left margin stats: Counter({u'': 32})
div_1 right margin stats: Counter({u'': 32})
div_2 left margin stats: Counter({u'': 32})
div_2 right margin stats: Counter({u'': 32})
p_3 left margin stats: Counter({u'0': 4960})
p_3 right margin stats: Counter({u'0': 4960})
Cleaning up manifest...
Trimming unused files from manifest...
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\david\appdata\local\temp\calibre_0.7.52_tmp_erwfjq\calibre_0.7.52__knjwo.mobi