I was strugling with this until i found a solution just now. (note i'm using windows, not sure if this applies to macs as well)
based on what i saw the artwork is still imbeded in the file, itunes just isn't showing it correctly. i found that if i right clicked on an individual song, set the tab to "artwork" it will show the correct artwork even if it isn't showing in itunes album view.
you can do either one or all of the ff:
1.)
go to music
select all songs (ctrl + a) right click (while all songs are selected),
select "get album artwork"
some will be fixed right off the bat, however for obvious reasons if itunes doesn't recognize the song, you won't get your artwork
2.)
go to music
select the songs view (so all songs will be listed)
right click the top most song
select "get info"
click on the artwork tab
then click next until you go through all the songs
i found that viewing the artwork and clicking next somehow refreshes the artwork for itunes.
this doesn't work for all though
3.) when all else fails: do it manually
go to music
select the album view (so you see which album doesn't have an artwork)
select a single song from the album
click on the artwork tab / copy the artwork, click ok
now select all songs from the album
select "get info"
paste the artwork to the lower right hand side (it says artwork)
then click ok.
hope this helps, been scratching my head over this for weeks.