The only thing I do externally is copy the new .wav files into the folder that is my Auto Import source. Then I enter MC and do everything else.
I view/manage the steps via multiple tabs: 1. Auto Import source folder, 2. File Conversion destination folder, 3. Library folder where the final files will reside (typically an Artist folder because I'm usually adding to an artist's tracks).
I've done the process two ways. The steps that I just used, where Analyze Audio ran only partially, were:
1. Externally, put the tracks in the folder where MC will Auto Import.
2. Via MC's File Location, view the Auto Import folder. Select all the .mp3 files and manually run Auto Import. (I suppose I could wait for it to do its thing automatically, but I have no sense of when that might be.) This is when Analyze Audio happens, but it omits some files.
3. Via MC's File Location, select all tracks and Convert from .wav to .mp3. The original .wav files stay where they were, while MC creates the new .mp3 files in a different folder.
4. Switch to the folder with the new .mp3 files, run Analyze Audio again to finish the rest of the tracks, then continue with tagging, etc.
OR, since I'm not getting (or understanding) the benefit of Auto Import, I now tend to do it this way:
1. Externally, put the tracks in the folder where MC will Auto Import, simply because it's the folder where I move new .wav files into the library, "auto" or not. But don't run Auto Import manually (it doesn't seem to run automatically, at least not promptly).
2. Via MC's File Location, go to that folder. Select all tracks and Convert from .wav to .mp3 (VBR Extreme). The original .wav files stay where they were, while MC creates the new .mp3 files in a different folder. Option "Leave original file, add destination file to library" is selected, so this step adds the files to the database.
3. Via MC's File Location, go the folder with the new .mp3s.
4. Select all the .mp3 files and manually run Analyze Audio. It works on all selected files. Does it matter that in this process Analyze is done to the .mp3 files not the .wav files? Is there possibly enough difference to matter to ReplayGain?
Maybe I'm misusing Auto Import, since I don't see it do anything "auto" and I'm not clear on why I'd ever want it to. Even if MC automatically did the one step of adding new files to the database, I always have several more manual steps, and via one step or another the files I'm working with get added to the database. Maybe Auto Import is for a different purpose?
BTW, my wish list is for a one-click process to convert/analyze/import a set of new files. But it's fine as-is, just the mystery behavior of Auto Import + Analyze Audio.