As to your question why your losing some HDD space... It's probably to do with Shadow copy storage as a small portion of your HDD is given over to storing shadow copies (usually around 15%). As the default defragger (which in my opinion is awful, slow and a complete waste of time) moves files around between the two then it may look like some has gone missing.
To resize your shadow storage check here:
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note: Don't go any lower than 900MB otherwise you may encounter problems..