Boot Camp drivers don't always load (for Windows 7)? Recently, I backed up my Windows 7 Boot Camp partition with Carbon Copy Cleaner before realizing that it would not be a bootable backup. Well, after some fiddling around, I made it bootable again (with the help of iPartition) and it generally works well.

However, for some reason, sometimes when I boot into Windows 7, it appears that some drivers don't work properly about half the time. For instance, if I load a game, the game will not be full screen and will instead be the exact dimensions that is specified (my display is 1920 x 1080; if the game is set to 1280 x 720, then it won't stretch to full screen but instead appear at that size). As I said, this happens about half the time.

Also, I use MacDrive so I can write to Mac partitions, and when these display problems occur, then MacDrive will also show an error saying that it needs to be repaired.

All of this can be fixed with a restart, but after restarting, my two displays will be duplicated instead of extended.

It appears that the display drivers (and perhaps a few things, related to MacDrive) don't seem to be loading properly at all times? For some reason, I can seem to fix this if, when in Mac, I quit all applications first before booting up Boot Camp. I don't know how they could be related, but it so far seems that way.
Whatever you do in OSX is completely unrelated in how W7/8 behaves. Unless one of the apps you are using is VMware Fusion (dont know if Parallels can do this too) to access the bootcamp partition as a VM. 

I would highly reccommend reinstalling the WindowsSupport files created from the Bootcamp Assistant to see if that fixes the problem.