I've manually input lyrics into over 3,000 songs in my iTunes. Then along came the updates. When I'm listening to my music on my iPod or iPhone, I only see lyrics from songs I've bought from Apple. None of my digitized CDs or downloads from other sources (such as Amazon) will display the lyrics. The only workaround I've found involves one sacrifice for another. Either I keep listing to music via iTunes on my iPhone, and get lyrics for about a 1/4 of the songs (if I'm being generous) OR I use a free app called Songbucket. With Songbucket, not only do I get my lyrics back, I can also choose the random pattern they play, as iTunes used to do. The sacrifice? Songbucket does not play music purchased from Apple.
For me, it's worth losing the minority of iTunes to have my lyrics back on 3/4 of my songs.
I'm still looking/hoping for a better solution, where all my music, with all my lyrics, are accessible in one player.