I usually post technology stuff on my Tested blog, but it's currently disabled due to high amount of blog spams; so I'm posting this problem-with-solution here. It may be of use to someone.

p.s. Please pardon the formatting of this blog post, Giant Bomb tools are borked during the writing of this post.

tl;dr: If you have problems exporting your bookmarks to HTML or syncing via Xmarks, just give your problematic bookmarks a 8+ character name.

To keep things simple (because I've done about 3 edits on this post, so far) here is what my problem was, what I used, and what happened:

• Strangely, and only recently, some of my bookmarks are missing.
• I used Xmarks to sync and backup my bookmarks. It may be Xmarks fault, so I uninstalled it.
• I thought my Firefox bookmarks database was corrupted. I repaired my bookmark database file by closing all my Firefox windows first, then deleted the "places.sqlite" file in my Firefox profile (located here (for Windows 7): %appdata%\mozilla\firefox\profiles - there should be a file with a strange named folder, that is your profile). It may be this problem, so I did this.
• Finally, after looking, comparing, and testing things in my bookmarks; I found that a bookmark (when exported via HTML or Xmarks) that does NOT have a name or has a name with 7 characters or less, does not actually get exported (weird, I know). If that bookmark is in a folder, the folder name is listed in the exported HTML/Xmark file though. (?!)

• So, I had to...
  
  1. Backup (via Backup or exporting to HTML in the Library window) my current updated bookmark file (with missing bookmarks)
  2. Lucky I had this: Restored my old bookmark file (with the missing bookmarks) (WARNING: Restoring from a backup file will replace all your bookmarks!!!)
  3. Opened all my previously missing bookmarks.
  4. You may skip this step, but just in case: I gave each, individual missing bookmark (that was missing in my updated bookmark file) a name (such as: "this is a bookmark")
  5. Restored to my updated bookmark file (with the missing bookmarks)
  6. Bookmark all the previously missing bookmark websites.

... ??? ... !!! ... Profit?