I will admit,
that particular detail isn't in there (it is now on my list to add further details about the options and a Troubleshooting section, but my list is long and my time is short). It is covered in brief elsewhere on the Wiki, but it is buried in other sections that are (much more) out of date.
However, kensn's tip is the answer, almost certainly.
MC ignores files you manually remove by default. That's because otherwise it would drive people nuts because you'd remove the files (but not delete them from disk) and then Auto-Import would instantly re-import them. To get it to import
everything in the specified directories, you can de-select that option. Also the drag-and-drop and Shell Extensions methods of Importing don't respect this rule and always import the files provided.
However...
I should note, if your
original goal (before you discovered this problem) was to remove the files in order to re-import them "fresh" then you'll be sad even when you get them re-imported, as they'll re-import just like they were before (or, pretty much). That's because of two factors:
1. MC tracks files you've deleted in the special, hidden, Removed database. This is how it does the Ignore Previously Removed Files trick, and it also allows for an (often convenient) undo. If you accidentally remove files (upon which you spent considerable time making the tags "just so") from your Library? Just re-import them. When MC does, it essentially "undeletes" them, so nothing gets lost.
2. MC automatically syncs a ton of metadata to the in-file tags, so it is essentially creating a little mini "database backup" within each file. This can be disabled if desired.
If you do need to remove files and import them fresh, there is a way. You need to remove them from this Removed database after you remove them from MC "proper". To do this, you need to make a special
Media View or
Smartlist that shows them:
http://yabb.jriver.com/interact/index.php?topic=72593.msg491631#msg491631