I have owned a Canon 5D Body for approximately 9 months and am
finding (intermittently) that once an aperture is set in either Manual
Mode or Shutter Peiority mode I cannot change it until I shut the
camera down and clear all "Function Settings" and other Settings and
turn the Canon5D back on.

Is it that I'm not knowing how to set things up properly or should it
go back to Canon under warranty ?

Regards,

Peter.