I don't believe it has no.
I haven't verified this yet, but I'm thinking that the version with the visible beak is the earlier season 2 version and the later "drone like" version is season 3 onwards and appeared as part of the image makeover which occurred in season 3 when they moved to Vancouver for filming.
The earlier version always appears to be red and (I think) seen mostly in season 2, although it is still seen on the ID cards.
Other than that I don't know why it changed. I was about to suggest it may have been a printing error which saw the area between the beak and bird filled with ink but I just noticed that the whole bird is different so it looks like a deliberate design change.


The blue logo with a drone like head seen from season 3 onwards.