Ah, yes those are the regular SATA ports on your board supported by the Intel chipset. The two eSATA (= external SATA) ports connected to the JMicron controller are on the rear panel of the motherboard. The JMicron SATA/PATA controller is an extra chip on your motherboard that gives you the two eSATA ports and a PATA connector. The two eSATA ports are normally used for external drive enclosures/docks with eSATA connectors. Since you were talking about eSATA, I wasn't sure which ports you were using. You'll need an eSATA to SATA cable if you're going to try plugging the drive into one of these ports, but it won't be practical if the drive is inside the computer case.
The six internal SATA ports are connected to the Intel ICH9R which is the southbridge part of the main chipset on the motherboard. Since you're using RAID, you've installed the Intel Matrix Storage Manager (or the newer Intel Rapid Storage Technology) driver, right? Which means the Intel driver (iastor.sys) is also handling the other internal SATA ports. The ICH9R is supposed to support RAID volumes up to 256TB, so I would think iastor.sys should be able to handle long LBA drives. But it's possible it isn't, or you're using an older driver version. You could try installing the latest Intel RST drivers. The latest version available on Intel's site is 188.8.131.522. There's a leaked 184.108.40.2061 WHQL beta driver on this site. The Intel driver can also be used in AHCI mode.
Be careful if you try these drivers on your RAID 0 install, messing with drivers when your boot drive is on a RAID 0 could leave you with an unbootable system. Backup your system first, or try them out on the test installation on the spare drive.
You should also try Microsoft's own default drivers (msahci.sys in AHCI mode or intelide.sys in IDE mode) that comes with Win7. But that means abandoning your RAID 0 config.
It's possible to replace the Intel RAID Option ROM in the BIOS with a newer version, but I can't say if that would help. You may find a modded BIOS for your motherboard around somewhere or mod it yourself, but modding the BIOS is a risky thing to do, you may end up with a dead motherboard. Since Win7 didn't detect the full capacity of the drive when you connected the drive after booting Win7, it's probably not a BIOS issue. You are able to boot now with the drive connected after you repartitioned the drive, right? Let's see how your tests go.