eSATA enclosure/BIOS weirdness

I have a tendency to ramble so let me try to do the tl;dr version right at the top:
Symptom: eSATA enclosure with 2 - 2TB drives connected to the same port where it was working in w7/w8 stops detecting the second drive after full-reinstall (w7) and internal HD shuffling to move SSD to SATA3/boot position.

I've done minimal testing so far, but was wondering if anyone had any experience with how those ports are generally laid out/use MB resources.

In BIOS I noticed that eSATA was set to IDE mode. When I switched it to AHCI my computer would go into a boot loop after getting to the Loading Windows Logo. "Run Startup Repair/Boot Windows Normally?"
This persisted even after I switched eSATA mode back to IDE in BIOS and disconnected the eSATA enclosure. I wasn't able to boot until I disabled eSATA entirely, which makes me think that my eSATA ports are somehow affecting the SATA chip my boot drive is on... somehow.
Or something else I'm entirely unfamiliar with. Googling has not been very helpful.

Gigabyte GA-x58a-ud7 v2.0
South Bride has 6xSATA2 - 2-Rear Panel Access, Front Panel Access, Bluray burner, 2x 1TB drives
Marvell 9128 has 2xSATA3 - 256GBSSD
JMicron JMB362 chip 2xeSATA - Enclosure w 2x2TB

I am still early in the troubleshooting process, but maybe someone has run into this kind of thing before?
Just realized that one of the things I HAVEN'T done is actually power-cycle the enclosure itself... that will be the first thing I do once I get back home, but the question stands since that shouldn't affect the boot cycle when it isn't connected to the computer. So there is definitely something strange going on still...

Finally decided to mess with this again instead of just making due without my main media library and found the solution.
My first mistake was looking at the Motherboard/Firmware level... apparently the port multiplication happens at the OS level.

My second mistake was in trusting that all the relevant drivers would be available from the Motherboard manufacturer's site.

After finding the updated driver download for the JMicron eSATA chip and loading it into windows suddenly my 4TB are back.