When using AppGameKit Classic I find that the GetScreenYFrom3D() function returns an inverted screen position value. I get around this by using GetVirtualResolution() - GetScreenYFrom3D().

However, I use AppGameKit Studio to target Vulkan and the GetScreenYFrom3D() function works normally (not inverted).

Is anybody else getting this problem?

Yes and I've also had to manually detect when in AKGC OpenGL vs AGKS Vulkan to calculate the difference for the correct position result. You may also encounter differences in OpenGL when a render image is active vs when the render is set to the screen.

Yes, I already noticed some differences with how you can use images created with CreateRenderImage(). For instance, I can't apply an image mask to them. Where I've been creating procedurally generated textures I have saved them to the file system and reloaded so I can apply the mask. Not a massive problem in my case though.

I have not experienced this problem

I'm using the most up to date versions (via Steam).