evga sr2 build problem - disk 0/1/2/3?

Hi All, this is my first post

I have the EVGA SR-2 motherboard.

It has SATA ports 0-5 (black) which are controlled by the Intel chip on the mobo which runs as SATA II (3gbps)

It also has SATA ports 6-7 (red) which are controlled by the marvel chip, which runs as SATA III (6gbps).

I want my system drive to be a pair of disks mirrored on the faster, marvel, controller and my data disks to be on the slower, Intel, controller. I also want to add/remove disks at a later date.

The problem:
I can install and run windows 7 x64 fine on the mirrored disks on the marvel controller, but as soon as I add a disk to SATA port 0,1,2,3,4 or 5... Windows doesn't boot. Instead it enters a cycle of booting to the scan and repair screen, where it decides the boot disk is corrupt and reboots the machine for another go.

If I cancel the scan before it is allowed to start, I can get to command prompt.

I then use diskpart to try to figure out the problem.

The best description I can give is: a whole lot of screwy going on. Basically what should be drive letter C is no longer the case.

I have tried:
Using diskpart to change drive letters, remove erroneous letters and prevent auto assigning, etc...
If I rebuild win 7 with all the disks in, then the system reserved partition ends up on a different disk to the os (even if I create and format the 2nd disk). No good for removing at a later date.

I think the problem is to do with the order in which the disks are handled by the os.

Essentially I am asking:
How do you install windows to disk 2/3/4/whatever, that will allow me to add/remove data disks as I fancy.

OR... How do I install an os to SATA port 5/6 and allow for other disks to be added/removed

OR... How do I prioritise the sr-2's Marvell controller over the onboard Intel controller (the BIOS does not seem to allow for this).

I used to be very hot on PC building between the 486 and P4 days. I have spent a massive amount of time catching up with all the latest and greatest and this mono has been a steep learning curve for me.
I have spent about a week trawling for answers... So, anyone got any ideas?

Make sure the Win7 HD is set first to boot in BIOS at all times.

Post back a screenshot of Disk Management - Post a Screen Capture Image

If it wont' boot then take a camera snap of Partition Wizard bootable CD drive map and listings with drives plugged as you prefer. Tell us what is on each. The flags make a big difference. However a hardware expert will need to advise on the Intel vs. Marvel priorities as these matter.

Generally it's best to have Win7 HD in DISK0 position so that no preceding Primary partitions - especially if they become marked Active - can steal the System flag and boot files during a reinstall or boot repair. But Marvell/Intel boards can't always conform.

Hey, sorry for delayed response.

I've recently discovered that there is a question over the performance of the sr-2's Marvell controller vs the Intel one.
I've spent the last couple of days bench marking a fresh build on both controllers.

I'm writing this one the train, so results are from memory.

Interestingly the marvel setup produces similar results seeking files under 512k, and is much quicker at handling file chunks up to 64mb over the intel.

The marvel is better at burst and sustained transfer rates across the whole mirror over the Intel.

The marvel seems to be much better. However it has one fatal flaw, in that every so often it will hang briefly during tests. The issue shows up in the results and consequently affects the "slowest" bench marks.

If I hadn't read general negative talk about this controller, I would say there was some sort of driver issue.

As it is the vibe on t'internet is that the marvel controller is bunk and you're better off disabling it.

I feel cheated, thank you marvel and evga.