It sounds like you need to add your Windows partition to your /etc/fstab file, and then it will be automatically mounted on start up. How about doing:
gksudo gedit /etc/fstab
And then add the following lines:
# Mounting Windows partition:
/dev/sda1 /media/Windows ntfs defaults,uid=0,gid=46,auto,rw,nouser,umask=007 0 0
So change sda1 to your Windows partition, and also make sure whichever directory you want to mount it to exists. In other words, in the above example the /media/Windows directory needs to exist so you can mount to it. You can create a directory with:
sudo mkdir /media/Windows
Anyway, let me know how that goes.