I have the same problem, I played with the agesetttings.exe and I the game resolution is always the one of my screen (native), I even changed directly the display.opt file to a custom one (by changing the screenwidht and height + fullscreen=1) but nothing do, I still have my native resoltion each time I am lauching the game.
my display.opt file is showing this:
ScreenWidth = 1366
ScreenHeight = 768
ScreenDepth = 32
ScreenFrequency = 60
Cursor = Software
FullScreen = 1
Windowed = 0
Borderless = 1
BrigthnessLevel = 0
MapBrigthness = 0
But when I play the game the resolution is 1920*1080 - full screen (my native resolution)
The "standard" / windows mode is working as normal, its only an issue with the fullscreen mode.
My configuration: win 7 on a nvidia GTX570m, playing with the latest BoA2 patch, nothing fancy or unusual.
Operating System: Windows 7 Home Premium 64-bit (6.1, Build 7601) Service Pack 1 (7601.win7sp1_gdr.130828-1532)
Language: English (Regional Setting: English)
System Manufacturer: Micro-Star International Co., Ltd.
System Model: GX780/GT780/GT780DX
BIOS: MSI GT780DXR E1761IMS Ver:3.09 08/04/2011 MSI-Notebook
Processor: Intel(R) Core(TM) i7-2630QM CPU @ 2.00GHz (8 CPUs), ~2.0GHz
Memory: 12288MB RAM
Available OS Memory: 12266MB RAM
Page File: 4761MB used, 19767MB available
Windows Dir: C:\windows
DirectX Version: DirectX 11
DX Setup Parameters: Not found
User DPI Setting: Using System DPI
System DPI Setting: 120 DPI (125 percent)
DWM DPI Scaling: Disabled
DxDiag Version: 6.01.7601.17514 64bit Unicode