I put in an interrupt function to handle Timer1/2 A1 interrupts and I see this in the assembly "4292 0382 0382 MOV.W &Timer1_A3_TA1CCTL0,&Timer1_A3_TA1CCTL0". Hopefully this helps. Looing at the value of TA1CCTL9 in the debugger, I see it is 0x0008. The other listed timer controls all have zero values (0x0000) except TA1CCTL9. This happens pretty much at startup.
Dan