The GOG version of BG&E doesn't look like it was patched to v 1.01.
The changelog includeded these fixes:
* Fix crash on processors without SSE. The game now doesn't crash when executed on processors whit no SSE support. Older Athlon/Duron processors doesn't support SSE extended instruction set.
* Antialiasing support. Users with fast graphic cards and almost 64MB of VRAM can enjoy full anti aliased graphic. To enable antialiasing run the "Beyond Good & Evil Settings" application, go to the "Advanced Setting" tab and move the "Antialiansing" slider to "On". WARNING: Do not force antialiasing on the graphic card control panel that will result on black screens and corrupted graphic.
* Shadows can be disabled. If you want to reduce further the VRAM consumption you can disable shadows.
* Lower screen resolution available. If you want to reduce further the VRAM consumption you can choose screen resolutionsunder 640x480
* Improved sun special effect. Now the sun special effect works on any graphic card and has a better behaviour.
* Improved water blur effect. Now the water blur effect works with no graphic glitches.
* Speed up water reflection. Now if you set the water detail to low you obtain a better speed up.
* General speed up. Changed many things to gain speed where possible.
Or was that already taken care of by the GOG wrapper or something ? I've purchased the game from GOG again but didn't had the time to test it properly :P
Just wanted to hear your thoughts on this.

I thought of that the other day, having the retail version of BG&E myself and remembering a patch. The GoG version is not patched but I remember that the 1.01 patch was not meant to be used by everyone due to some issue that I don't remember.
However It cannot be installed on GoG version so I think GoG team should verify if it improve something and maybe release a standalone patch for their version.

An issue with the patch you say ? Maybe issues with a certain series of graphics card. I remember that PoPSoT had issues with Nvidia geforce 6800 gfx cards. They released an official fix for this. Considering both games are running on the same engine, it could be linked.
It should not be installed on the GOG version! It would reintroduce the cd check :\ , only way to profit from the patched exe.
Disable shadows ? Where do you see that option ?

You have to open the "Beyond Good and Evil Settings" application and click on the "advanced" tab. Here you will find several graphical options including changes to the shadows.

Yes, I'm aware of that, but I fail to see the option where you can disable/turn off the shadows.
EDIT: I opened "SettingsApplication.exe" with ResHack and looked into the dialogs. Looks like German and Spanish don't have the option to turn Shadows off. I have a german OS, so I naturally get the german version :P
2nd EDIT: Ok, I fixed it and now the option works again for german and spanish users. So, if anyone is interested...

I have an original box version, so I remember 1.01 was unplayable without cheats because there was one really bad bug in one area. Some important key doesn't fall down from roof as in 1.00 and you were stucked in that area. Only solution was using of cheat or just play fine 1.00 version.
So, I think this is 1.00.

Yep, the key in the Slaughter House Central Hall didn't fall from the ceiling. There was a savegame fix as a solution.
1.01 patch solved that but also generated another bug, namely you can not leave the Central Hall.
The same fix (or an updated one :)) did the trick. Whoever might bump into it:
[url=]http://www.terrygoodkind.net/~rahly/bgae.php[/url]

I contacted GOG support and they mentioned:

Oh great, thanks! It's just that users with either a german or spanish OS don't become to see that option. So at first I couldn't deactivate shadows in my app. Therefore I suspected it not being the up-to-date version of the game.
I edited the settingsapplication to reenable the option for german and spanish users though.
They somehow forgot to patch those two languages maybe ? Seems odd.