I have a collection of MP3 ripped from my original CDs. Most of them have covers.
I found that my Windows Phone 8 didn't have many covers at all (perhaps 10%) when transferred via the Windows Phone Desktop app for Windows 7.
When manually copying those files or if using the Windows Media Player to sync then covers appear ok.
Of course these all work really well with Zune Desktop and Windows Phone 7.
Once again, I am not sure it's a good move to release such a buggy Windows Phone Desktop app. It should at least have feature compatibility with Zune Desktop.