I'm a long time Linux user and have minimal experience with Windows. That being said, I bought a Nvidia GT 730 and Windows 7 Ultimate yesterday to play a new game. This doesn't have anything to do with playing the game; it happens all the time.
In Linux, I use the Intel HD Graphics 4600 (i7-4770) for both monitors without any problems.
The monitor configuration is 1920x1200 on the primary and 2560x1440 on the secondary. In Linux, the primary is connected via HDMI and secondary via DP. In Windows, they are both connected via DVI.
Getting back to the problem on Windows:
I've installed the latest Nvidia 346 drivers, and they are working properly. Resolutions on both monitors are detected correctly (no EDID problem), and the primary (1920x1200) looks perfect. The secondary (2560x1440) looks like garbage. The secondary resolution is set to 2560x1440, which the Nvidia control app properly detects as the native resolution. Text is barely readable.
Native 2560x1440 resolution:
Next lowest 16:9 resolution, 1920x1080:
I'm having trouble figuring out what could possibly be happening. I've tried all kinds of searches for similar problems, and I'm coming up empty. Unfortunately, my lack of Windows and even discrete GPU experience is causing me trouble. Any help would be greatly appreciated.