Hey everybody. I'm not sure if this problem has been encountered by anyone except for me; but I imagine it has. I wanted to post my solution to it as it might be of some help.
This was my experience using Virtualbox 4.0.4 and ArchLinux running Gnome 3 and updated through the month of April 2011:
I'm using Virtualbox with Arch Linux as the host and a Windows 7 guest that is installed on a different physical partition. In going through the process of setting VBox up to use the physical partition, I first installed Windows 7 normally and then created a drive for Virtualbox that looked unto that partition (Following the prescribed process in the manual). However, upon installing Guest Additions I also installed the experimental 3D driver that requires booting into safe mode to do so. This is what caused problems for me. After this was installed, nothing that required DirectX would run properly when booted directly into Windows 7. At the time, I could not figure out why and after several hours of trying things and a reinstall of Windows, I finally figured it out.
So if you plan to play games or use other graphics intensive applications when booting into the physical Windows 7 install, DO NOT install the direct3D driver with Guest Additions.
Of course, there may be a work-around for this; but I am not aware of one.