Okay, I opened up LR using the "bad" catalog. The "bad" behavior continued WRT to "dropping-back-two-levels-but-actually-in-real-life-on-the-actual-file-system-putting-the-file-in-the-"right"-place" if you get what I mean.
Then, as I think you suggested, I tried hitting Import and, on the destination side, choosing "Create New Folder" as a subfolder in the hierarchy. Same bad outcome. Instead of placing the folder (The catalog folder) in the proper hierarchy, it drops it two levels up. However, checking in the actual FS, the folder is, in fact in the correct place.
IOW, in the catalog, my new folder Test 5, is represented as Master_Images/Test 5. Whereas in the Mac FS, it's correctly located in Master_Images/Recent/2012/Test 5.
Now, here's where it gets fun. Creating yet another folder totally OUTSIDE the Master_Images Hierarchy, on a different drive, creates the proper representation in LR and in the FS. IOW, I create a folder, Test 6, and put it in Startup/Users/marshall18/Desktop and, bingo, it's properly displayed in LR.
Soooooooo. Your thoughts? BTW, this is LR 4.2RC on OS x 10.8.2 12c37, 43, and 50 and, I believe, also 10.8.1.