thork:
...
I wish I understood a little more how a running timer interferes with setting the registers ...
The Arduino init() function (in wiring.c) sets Timer1 to 8-bit Phase Correct mode so that analogWrites to the Timer 1 pins will be consistent with analogWrite calls to other timer OCR pins. In the 8-bit mode, the OCR1 register is (automatically) updated with its upper bits equal to zero every time the timer times out.
If you are going to be using any timer for anything (anything at all) you will be reading through the ATmega data sheet and you will be initializing the TCCR registers to whatever you need them to be so you won't have to worry about unknown states of your timer that were set up by the (invisible-to-"normal"-users) Arduino initialization code.
Regards,
Dave