I'm having the same problem too. My 2nd monitor is a Samsung LED TV - and there seems to be no rhyme or reason to why this is happening. It's a new 27in iMac (Radeon HD 6970M, 3.1 GHz Intel Core i5) and i'm using a displayport/thunderbolt to HDMI converter for the 2nd screen.
This seems to happen only on my primary monitor, although more often than not I'm playing video on the 2nd.
Initially I cursed the magic mouse, thinking it had lost connectivity, but it's always there - just invisible. Move it to the TV and it's back again. Move to the iMac and it quickly vanishes again.
I never had this problem with my old 2007 24in iMac
This is random though - not all the time, so i'm stumped as to the cause.
Looking forward to a fix as it's getting right on my thruppeny bits....