I may be misunderstanding the question, but maybe this will help:
Under "Tools -> Options," in the File Location area, under Track Images Location, what settings are you using?
If you have it set to "Next to file (folder.jpg)" then your image will get renamed folder.jog and get stored in the appropriate folder (next to the file or files it belongs with). However, if all of your new music files are in the same folder, then every time you add more cover art, the cover art will keep replacing itself (because it's all named folder.jpg) and will associate with everything in that folder.
For that reason, I'd suggest using the "Tools -> Options -> File Location -> Track Images Location" option of "Next to file ([Artist] - [Album].jpg)" so that the cover art names are more likely to always be unique and don't over-write each other .... and resist adding cover art images until the art has been stored and moved to it's final resting place on your hard-drive (so you'll be less likely to orphan cover art in odd folders while using MC to batch-rename/organize the music files).
The benefit of the "In specific folder" option, though, is that all of the cover art stays in one MC cover art folder, with the art staying associated with the proper files at all times.... I prefer the "next to file" options, however, because it allows me to move the art and music files all at once when needed (to another hard drive or burning everything to a disc, etc.).
The one problem I've had with this (saving "next to" instead of in the specific cover art folder) is that MC doesn't always recognize the cover art file in the folder automatically -- you have to manually tell MC to associate the art with the music ("Image -> Quick Find in File/Cover Art Directory" does not appear to quick-find and associate cover art that is stored next to the music in the same folder, unless I'm doing something wrong).