We have discovered another problem with iTunes 11.0.3. It seems that when we use Apple Scripting Bridge to ask iTunes whether or not it is in Shuffle mode, the answer now is always NO. Therefore, BitPerfect now has no way of knowing whether or not iTunes is in Shuffle mode!
This is only really a concern from the perspective of Gapless Playback. When BitPerfect detects that iTunes is in Shuffle mode, it temporarily disables Gapless Playback. But if it thinks Shuffle mode is still off, it won't do that. The net result is that it will pre-load the wrong track into memory. When the current track finishes, the (wrong) pre-loaded track starts playing for a brief moment before BtPerfect realizes that iTunes wants to play a different track.
The only work-around I know of at this time is to temporarily check "Disable Gapless Playback" in BitPerfect's Preferences menu every time you enable iTunes' Shuffle mode.
This problem may also affect iTunes 11.0.2 as well, but I can no longer test that.