Yep, just found this post when i was googling if only I had this problem too .. it just began after the latest 45,0 update, the browser window NORMALLY stays transparent for 1-2 seconds on each startup i think, but it has happened that i have needed to restart Opera several times to get it to work..
Need to say that it happens on a rather old Windows 7 (64 bit) pc, but i haven't seen this behavior on Win10, maybe something that is not optimized for old systems