Hmmm.... It should NOT be doing that, but I've seen something similar in the past. Perhaps something is a little broken again in Auto-Import land with the Ignore previously removed setting. In any case, do this:
1. Make a new Smartlist and call it Deleted Items (or something similar).
2. With the Edit Smartlist dialog open, hit the Import/Export button.
3. Paste this into the rules data dialog that appears:
~d=r ~sort=[Filename]
4. Say OK, OK and look at your new smartlist.
You should see your files in the list (I sorted it by filename, so they'll sort like they are on your C drive or whatever).
Find them in the list, select them, and delete them again. When it asks, pick "Remove from Media Library" (NOT one of the "and send to or and delete" options). That should get them out of MC's "memory" and make it re-import them like they're fresh and new. Let us know if this happens though, because assuming that Ignore previously removed files option really is deselected for the folder they're now in under Auto-Import, then this shouldn't happen and maybe something is broken.
If after you do those steps, you DON'T find the files in the list, then it is likely that MC has actually re-imported them, but imported them with the same old "bad" metadata (unknown [Media Type] probably) as before. If this is the case, ask and we can help you get that sorted quickly and painlessly.
This is possible precisely because MC does track the files it deletes after it deletes them, using that special "hidden" database that I just showed you how to "see". When you import a brand new file, MC analyzes it and decides what kind of file it is and does all sorts of other work to get it imported. But, if you delete a file, but then later re-import that same file, MC checks this deleted items database for two reasons. First, it checks it to see if it should re-import it at all in the first place. If you have the "Ignore previously removed" option turned on, then it doesn't at all and the file is ignored. Second, if "Ignore previously removed" is turned off, then MC restores the information from that deleted record instead of re-importing the file from scratch (and re-doing the analysis and all of that). This makes sure you don't lose any intentionally set metadata that wasn't (for whatever reason) explicitly written to the files' tags, and it also makes the re-import process quicker and less painful on system resources (every little bit helps).
But, it could have bitten you here.