Tell me, when you import the new files, do you get all the tags you had for the previous versions, even custom tags if you have any?
If so MC is finding the record of the previous files in its "Removed" database and is reusing the tags from those files, as it is supposed to. I would only expect MC to do that if the file name stayed the same though. i.e. The original files was a 128Kbps version of "I'm Happy.mp3" and you replaced it with the 320Kbps version of "I'm Happy.mp3". If you were ripping to FLAC so that the file name changed to "I'm Happy.flac" I would not expect MC to do that.
If the tags are being picked up from the Removed database for the new file version, then the file would already have values in the appropriate Audio Analysis tags. Hence MC wouldn't re-analyse them, as it thinks that has been done.
You could delete the records of the original files from the Removed database before importing the new ones, but then you would lose the benefit of picking up the existing tags. That may or may not be important to you. You can use a Smartlist to find the file in the Removed database.
You could also delete the contents of the Audio Analysis tags before deleting the original files, but that is as much work as any method.
I think I would just do what you have been doing, and use the Recently Imported Smartlist to find and analyse the new files.