MSI GT60 with Vertex 4 SSD - Freezing, won't load Windows only in SATA III port

Hello,
New to the world of SSD's and trying to get my Vertex 4 to be able to operate at 6 Gb/s. I know that in my MSI GT60 that it has to be in port 1 because that is where the SATA III controller is, port 4 is just a SATA II. I was able to update the Vertex 4 to firmware version 1.5 and when it is plugged into port 4, no issues at all. It will run and take anything i throw it while running at 3 Gb/s in SATA II mode. My port 1 currently houses a 500gb Western Digital Scorpio drive.
As soon as i throw the Vertex 4 in port 1, issues arise. Sometimes i get a disk read error right after bios, sometimes it just freezes. On the latest Intel RST for my board, 11.2.0.1006 it can actually boot on occasion but 90% of the time freezes but still only reads 3 Gb/s when it does boot. It does the same thing in version 11.1.0.1006 and any older RST it just freezes or says disk read error and never boots.
I have my bios set to AHCI mode and i have tried the Vertex 4 by itself and also with the WD 500gb in the other port. When i switch back to Vertex 4 in port 4 and WD in port 1, no issues at all. Just trying to see if this is a known issue or anything else i can look at. I made sure to break the RAID 0 and it was a clean install of windows 7 to the drive.
Running on bios E16F3IMS.10M. The Vertex 4 is at its latest firmware as well. I do have one PCI device i can't identify in Windows and thinking it might be the issue but can't narrow it down. I have the Intel RST installed.
I also posted this on the OCZ forum and did their tips as well.
Thanks!
James

Hi everyone, I've still the problem with my windows 8 or my windows server 2012 installed on disk on vhd file.
I've putted on an other kingston ssd on sata2 and there is no problem! crazy

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https://forum-en.msi.com/index.php?topic=143558.0

Quote
The problem appears to be the drive (WD WD1002FAEX 1TB).
It is a firmware issue with the HDD (or the drive itself is faulty). WD may have a fix for it. Your revision is possibly a 01 series, & the 05 series work fine. I will search for the thread with the exact revisions details & edit my post with it.
Quote
They found that there are two versions of WD1002FAEX in the market. They are with firmware version either 01.01v01 or 05.01D05. The Marvell chipset can detect SATA III (6Gb/s) for the WD1002FAEX with 05.01D05 but only 3Gb/s for WD1002FAEX with 01.01v01.

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