I had a problem - AAC protected songs I purchased back in 2006-2008 timeframe where being cut short, truncated, when played back. The file size and duration where not affected. It occurred when I copied the files to a backup external drive and then tried to copy them back to the local drive.
Solution: From itunes, I when to the "Show in Windows Explorer" selection, then I right clicked on the file name and selected "rename" Even thought I could not see the three character extension from that screenm I just added .m4a be sure to include the dot. This changed the true file name to be songname.m4a instead of songname.m4p which is what the protected ones were. Best of luck.