Won't boot unless I change SATA ports

This is a really weird problem. I have three MSI A78M-E35 motherboards with AMD A6 6400K APU's. I have 500GB Western Digital Blue hard drives hooked up in each of them. Loaded Windows 7 64-bit perfectly fine. Loaded all the drivers, software and updates. It's a very basic build. When I shut one of them down and unplug it for about an hour or longer, when I turn it back on, it begins "loading windows" and then reboots. If I use disable automatic restart on system failure, it doesn't show me a BSOD. It just reboots. When I run startup repair, the first five times, it tells me that unspecified changes to the system may have caused the issue and that it can't repair it. Any time after the fifth time, it tells me that boot status indicates that it booted successfully. The only way I can get the system to boot again is by taking the SATA cable and plugging it into another SATA port. Then it works again.. for a short period of time. After a couple times of turning it off, it's back to it's old ways again. I have loaded two of these three systems with IDE mode AND with AHCI mode, the issue still persists. I had a total of ten of these particular builds. 7 of them work perfectly fine, but these three are giving me this issue. I called MSI and they told me that the boards are defective (of course) and that I should RMA them. I do not believe that this is the issue. I appreciate any help that I can get on this.

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More about boot change sata ports
  1. A Windows build will include only the drivers necessary to boot in the sata mode that the bios is set with at build time.
    If the sata mode is AHCI when trying to boot and the windows install was done when the sata mode in the bios was IDE it will not boot because the driver support is not there.
    The converse is true too.

    It probably does not apply here, but AHCI is a subset of raid.

    Some motherboards have more than one sata driver chip or capability.
    That might explain work/no work differences, depending on the boot port.
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