could you try this one:
http://www.mediafire.com/?qumyaii2m2ni suggest, firstly disable folder.jpg from the artwork preferences, and tick and set Cover.jpg as the organised artwork preference.
Then just choose one folder from the computer section, right click and rescan the files then check the behaviour for one of those files is as expected.
It should now:
- put linked images first in the artwork list ie. first one is the primary picture
- if it exactly matches the embeded image (which it doesnt in your case), they will be merged so you will see one picture (but marked as being saved to both places)
- if disabled from preferences, folder.jpg will be ignored
- otherwise if folder.jpg exactly matches existing picture, merged otherwise added to end of artwork list