With iOS6, I too stared noticing missing album artwork in cover flow mode on my iPhone 4S. Pretty annoying considering I keep my entire iTunes library and synced playlists' meticulous. In my case, about 10% of my synced songs stopped showing artwork after my iOS6 upgrade. (And this included some albums downloaded directly from iTunes, go figure). I'm on a Mac running 10.7 but would imagine that this workaround method should work on a PC as well.
• First, I located each offending song/album on my iPhone 4S that was missing album art from showing in coverflow mode
• In iTunes now, I located those particular songs/albums and dragged its album art (copied it) to my desktop. (More offen than not, the album art file will be in .jpg format)
• Back in iTunes, I deleted the album art from those offending songs/albums
• For this next step I used Photoshop CS5 (but any CS version should work): In Photoshop, I opened the album art that was saved to my desktop and simply re-saved the art file back over itself (as RGB, 72dpi, baseline standard option from the jpg "save as" dialogue box (performing a very basic "save as")
• Back in iTunes on my computer, I then highlighted the offending tracks and dragged/applied this newly re-saved song/album art back onto the offending album song files.
• After re-syncing my iPhone to iTunes, all offending song/album art was finally there again on my iPhone 4S iTunes in coverflow mode
Now while I realize that not everyone will have access to Photoshop, many imaging software applications that can be downloaded to Macs & PCs, come with free 30-day trials. All of these applications should be be able to perform the same, simple "save as .jpg" command that I used. Good luck.