After some digging my real question turned out to be why windows only recognized roughly half the size of my hard drive. My original text:
On my 2 TB data disk I have two primary partitions, one of 1.6 TB for data storage in Linux (ext3) and one of 300 GB for some additional data storage for Windows. I run a dual-boot Windows 7/Ubuntu 12.04 install.
The issue I have that if I start my computer into Windows 7, bot the partitions on my 2TB data drive are not recognized. In stead, Windows 7 sees one 1TB partition with type RAW. However, if I reboot to Linux, and then back to Windows 7, the partitions are correctly recognized.
The following two screenshots illustrate my situation. Before I reboot to linux:

and after the reboot:

I have two questions:
- What could cause this behavior?
- How can I solve this issue.
Edit: The following two changes did not solve the issue: 1. I replaced the grub bootloader by the standard windows 7 bootloader 2. I replaced the two partitions on the data drive by one ntfs partition.
So the system is now a single boot windows 7 system, and it still does not recognize the 2 tb ntfs partition, but insists that it is a 950 gb RAW partition.
Edit: When I removed the partition with gparted in ubuntu, Windows saw unpartitioned space, but only 950 GB (roughly half the size).