Experiencing same problem (Opera always on foreground whether on primary or secondary monitor):

Version: 25.0.1614.63 - Opera is up to date
Update stream: Stable
System: Windows 7 64-bit (WoW64)
Browser identification
Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/38.0.2125.104 Safari/537.36 OPR/25.0.1614.63

Same here. On Windows 7 x64, with Opera 24:

Main window is always on top of other applications (in full-screen and also in windowed mode)
In full-screen, I can't access my Windows auto-hidden taskbar.

And just as said Mesecur before me, it prevents me too from working efficiently, and I would add that it's a very big annoyance. I was defenitely happier back when Presto was still here...