Tried to rip my first CD since upgrading to 4.0.6: The Smashing Pumpkins: Oceania.
During the last track, a dialog popped up saying (something close to) "Error ripping track 13; this dialog will auto dismiss in 10 seconds". Dialog went away, rip finished, and an almost identical dialog popped up (just not auto dismissing). Checked with CUETools: track 13 ripped incorrectly.
Tried again: track was ripped identically, and a third time. And there were no obvious read errors: the rip didn't pause or retry at any point.
Reverted back to 4.0.3 (again: 4.0.5 didn't work for me, either, but for a different reason!), and the entire CD ripped perfectly (CUETools verified) first time.
I have the feeling that MM's core functionality is being compromised in favour of new (and, to me, unimportant) functionality. I guess I'll be sticking with 4.0.3 for quite a while, as it seems to work perfectly for me -- if I stick with CUETools for rip verification!