OK, I figured out why this happened. I have two libraries on my computer, one with local mp3s (original "itunes library") and one that points to the lossless music on my external harddrive ("external portable library"). When I previously transfered my purchases to the computer, I had itunes open with the "itunes library." When I plugged in the ipad today, I had the "external portable library" open. I am an idiot.