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The PCH component in the H67 chipset provides six SATA ports. This includes two SATA III 6Gb/s ports (the two blue SATA connectors on these boards) and four SATA II 3Gb/s ports (the two black SATA and two red eSATA connectors on these boards). The only difference in a PCH SATA port's configuration when used for eSATA is the enabling of hot swap on the port. The BIOS for the DH67BL and DH67CL boards provides support for booting from drives connected to any of the PCH's SATA ports. The fact that some are eSATA vs. SATA makes no difference from a boot standpoint.
I understand that you are concerned because one of the (I presume blue) SATA ports doesn't seem to be working any longer. I wish I could alleviate your concerns completely, but the fact is, the problem could be something in the supporting circuitry for this port or something in the port's implementation in the PCH silicon. It is more likely to be in the supporting circuitry, however. Really, all you can do is avoid using the bad port. If the problem is in the PCH silicon, you could eventually see additional failures (not necessarily isolated to SATA ports).
Hope this helps,
As always, you are a fountain of knowledge.
Yeah, I knew there were actually six ports, with the sixth being the eSATA one on the I/O plate.
I now recognize that (yes, blue) port 0 has been causing trouble for a long time. One of my previous posts regarded a 530 SSD exhibiting write errors when updating Linux. I always blamed the SSD, but now I think it was the port all along. One of the many strange things is that I don't see a chkdsk during the part of installation where files are being copied and compiled, only after the auto-reboot. Oh well, like you said, I'll just avoid port 0.
I'm adding a footnote just in case anyone reads this thread. My solution is to install using one of the SATA II ports, install all updates and applications, and then switch the cable to the right blue port (port 1). So far, no errors during use.