I checked for the occurence of TCCR3A being used elsewhere in the project, and this is the result I get with the reference check;
There are 8 matches, all of which are in the Timer3 library.
You will notice in the image the function disablePwm(..), where TCCR3A bits are cleared, but this function is not called in my program.
In the search section, line 26 is part of the Timer3 initialise function.
There's some smokey black magic happening in there somewhere.....
Paul